Manhattan and Q-Q plot¶
Load gwaslab¶
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import gwaslab as gl
import gwaslab as gl
Load data into Sumstats Object¶
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mysumstats = gl.Sumstats("t2d_bbj.txt.gz",
snpid="SNP",
chrom="CHR",
pos="POS",
ea="ALT",
nea="REF",
neaf="Frq",
p="P",
build="19",
verbose=False)
mysumstats.fix_chr(verbose=False)
mysumstats = gl.Sumstats("t2d_bbj.txt.gz",
snpid="SNP",
chrom="CHR",
pos="POS",
ea="ALT",
nea="REF",
neaf="Frq",
p="P",
build="19",
verbose=False)
mysumstats.fix_chr(verbose=False)
Create Manhattan plot and QQ plot¶
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mysumstats.plot_mqq()
mysumstats.plot_mqq()
2024/10/29 17:25:41 Start to create MQQ plot...v3.5.0: 2024/10/29 17:25:41 -Genomic coordinates version: 19... 2024/10/29 17:25:41 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:25:41 -Raw input contains 12557761 variants... 2024/10/29 17:25:41 -MQQ plot layout mode is : mqq 2024/10/29 17:25:42 Finished loading specified columns from the sumstats. 2024/10/29 17:25:42 Start data conversion and sanity check: 2024/10/29 17:25:43 -Removed 0 variants with nan in CHR or POS column ... 2024/10/29 17:25:44 -Removed 0 variants with CHR <=0... 2024/10/29 17:25:45 -Removed 0 variants with nan in P column ... 2024/10/29 17:25:45 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:25:45 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:25:46 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:25:47 -Converting data above cut line... 2024/10/29 17:25:47 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:25:47 Finished data conversion and sanity check. 2024/10/29 17:25:47 Start to create MQQ plot with 12557761 variants... 2024/10/29 17:26:00 -Creating background plot... 2024/10/29 17:26:19 Finished creating MQQ plot successfully! 2024/10/29 17:26:19 Start to extract variants for annotation... 2024/10/29 17:26:20 -Found 89 significant variants with a sliding window size of 500 kb... 2024/10/29 17:26:20 Finished extracting variants for annotation... 2024/10/29 17:26:20 Start to process figure arts. 2024/10/29 17:26:20 -Processing X ticks... 2024/10/29 17:26:20 -Processing X labels... 2024/10/29 17:26:20 -Processing Y labels... 2024/10/29 17:26:20 -Processing Y tick lables... 2024/10/29 17:26:20 -Processing Y labels... 2024/10/29 17:26:20 -Processing lines... 2024/10/29 17:26:20 Finished processing figure arts. 2024/10/29 17:26:20 Start to annotate variants... 2024/10/29 17:26:20 -Skip annotating 2024/10/29 17:26:20 Finished annotating variants. 2024/10/29 17:26:20 Start to create QQ plot with 12557761 variants: 2024/10/29 17:26:20 -Plotting all variants... 2024/10/29 17:26:21 -Expected range of P: (0,1.0) 2024/10/29 17:26:22 -Lambda GC (MLOG10P mode) at 0.5 is 1.21283 2024/10/29 17:26:22 -Processing Y tick lables... 2024/10/29 17:26:22 Finished creating QQ plot successfully! 2024/10/29 17:26:22 Start to save figure... 2024/10/29 17:26:22 -Skip saving figure! 2024/10/29 17:26:22 Finished saving figure... 2024/10/29 17:26:22 Finished creating plot successfully!
Out[3]:
(<Figure size 3000x1000 with 2 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
gl.plot_mqq() Options¶
Layout mode¶
If plotting all variants, it may take several minutes. You can use skip to skip variants with low MLOG10P in the plot.
Note: use verbose=False to stop printing log and use check=False to skip sanity check for mqq plots
4 patterns of layout:
mode= "mqq"(default)mode= "qqm"mode= "qq"mode= "m"
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mysumstats.plot_mqq(skip=3,cut=20,mode="qqm",check=False, verbose=False)
mysumstats.plot_mqq(skip=3,cut=20,mode="qqm",check=False, verbose=False)
Out[4]:
(<Figure size 3000x1000 with 2 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
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mysumstats.plot_mqq(skip=3,cut=20,mode="m",check=False,verbose=False)
mysumstats.plot_mqq(skip=3,cut=20,mode="m",check=False,verbose=False)
Out[5]:
(<Figure size 3000x1000 with 1 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
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mysumstats.plot_mqq(mode="qq", fig_args= {"figsize":(1,1)},check=False,verbose=False)
mysumstats.plot_mqq(mode="qq", fig_args= {"figsize":(1,1)},check=False,verbose=False)
Out[6]:
(<Figure size 200x200 with 1 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
Y axis¶
skip¶
skip: skip the variants with low -log10(P) values for plotting
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mysumstats.plot_mqq(skip=5,mode= "m", check=False ,verbose=False)
mysumstats.plot_mqq(skip=5,mode= "m", check=False ,verbose=False)
Out[7]:
(<Figure size 3000x1000 with 1 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
cut¶
cut : scale down the -log10(P) for variants above a certain threshold
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mysumstats.plot_mqq(cut=20 ,mode= "m",check=False,verbose=False)
mysumstats.plot_mqq(cut=20 ,mode= "m",check=False,verbose=False)
Out[8]:
(<Figure size 3000x1000 with 1 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
Make the Y axis jagged to indicate that it has been rescale.
jagged¶
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mysumstats.plot_mqq(skip=3,cut=20, jagged=True,mode= "m",check=False,verbose=False)
mysumstats.plot_mqq(skip=3,cut=20, jagged=True,mode= "m",check=False,verbose=False)
Out[9]:
(<Figure size 3000x1000 with 1 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
X axis¶
use_rank¶
use_rank: if True, GWASLab will use position rank instead of the physical base-pair positions for x aixs.
There will be no gap if use_rank = True
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mysumstats.plot_mqq(skip=3,cut=20,use_rank=True,mode= "m",check=False,verbose=False)
mysumstats.plot_mqq(skip=3,cut=20,use_rank=True,mode= "m",check=False,verbose=False)
Out[10]:
(<Figure size 3000x1000 with 1 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
xtight¶
xtight=True can be used to remove the padding
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mysumstats.plot_mqq(xtight=True, skip=3,cut=20,mode= "m",check=False,verbose=False)
mysumstats.plot_mqq(xtight=True, skip=3,cut=20,mode= "m",check=False,verbose=False)
Out[11]:
(<Figure size 3000x1000 with 1 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
chrpad¶
chrpad: adjust space between each chromosome by max(POS) * chrpad
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mysumstats.plot_mqq(chrpad=0.2,xtight=True, skip=3,cut=20,mode= "m",check=False,verbose=False)
mysumstats.plot_mqq(chrpad=0.2,xtight=True, skip=3,cut=20,mode= "m",check=False,verbose=False)
Out[12]:
(<Figure size 3000x1000 with 1 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
Annotation¶
anno=True¶
anno=True : annoatate all lead variants with chr:pos
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mysumstats.plot_mqq(skip=3,cut=20,anno=True,mode= "m",check=False,verbose=False)
mysumstats.plot_mqq(skip=3,cut=20,anno=True,mode= "m",check=False,verbose=False)
Out[13]:
(<Figure size 3000x1000 with 1 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
Since there are a large number of novel loci, if we annotate all loci, it will be too messy. Let's only annotate the loci with P<1e-20 by specifying sig_level_lead=1e-20.
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mysumstats.plot_mqq(skip=3,cut=20,anno=True, sig_level_lead=1e-20,mode= "m",check=False,verbose=False)
mysumstats.plot_mqq(skip=3,cut=20,anno=True, sig_level_lead=1e-20,mode= "m",check=False,verbose=False)
Out[14]:
(<Figure size 3000x1000 with 1 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
anno="GENENAME"¶
anno="GENENAME": automatically annoatate the nearest gene name
Note: remerber to set build=19 or build=38 when loading or plotting.
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mysumstats.plot_mqq(skip=3,cut=20,anno="GENENAME", sig_level_lead=1e-20,mode= "m",check=False,verbose=False)
mysumstats.plot_mqq(skip=3,cut=20,anno="GENENAME", sig_level_lead=1e-20,mode= "m",check=False,verbose=False)
Out[15]:
(<Figure size 3000x1000 with 1 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
You can specify anno_gtf_path to use you own GTF file for GENENAME annotation
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# mysumstats.plot_mqq(anno_gtf_path="/home/yunye/.gwaslab/Homo_sapiens.GRCh37.87.chr.gtf.gz",anno="GENENAME")
# mysumstats.plot_mqq(anno_gtf_path="/home/yunye/.gwaslab/Homo_sapiens.GRCh37.87.chr.gtf.gz",anno="GENENAME")
anno_d¶
We can use anno_d to slightly adjust the arrows.
anno_d accepts a dictionary of index of annotation: left/right
For example, 1:"left" means to adjust towards left.
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mysumstats.plot_mqq(anno_d={1:"left",2:"right"}, skip=3,cut=20,anno=True, sig_level_lead=1e-20,mode= "m",check=False,verbose=False)
mysumstats.plot_mqq(anno_d={1:"left",2:"right"}, skip=3,cut=20,anno=True, sig_level_lead=1e-20,mode= "m",check=False,verbose=False)
Out[17]:
(<Figure size 3000x1000 with 1 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
anno_scale¶
We can also use arm_scale to adjust where to put the annotation texts.
For example, arm_scale=1.2 means the default length will be multiplied by a factor of 1.2.
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mysumstats.plot_mqq(arm_scale=1.2, skip=3,cut=20,anno=True, sig_level_lead=1e-20,mode= "m",check=False,verbose=False)
mysumstats.plot_mqq(arm_scale=1.2, skip=3,cut=20,anno=True, sig_level_lead=1e-20,mode= "m",check=False,verbose=False)
Out[18]:
(<Figure size 3000x1000 with 1 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
arm_scale_d accepts a dictionary of index of annotation: arm_scale
For example, 1:1.2 means to adjust the arm of the second by a factor of 1.2.
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mysumstats.plot_mqq(arm_scale_d={0:0.8,
1:0.7,
2:0.6,
3:0.8},
skip=3,cut=20,anno=True, sig_level_lead=1e-20,mode= "m",check=False,verbose=False)
mysumstats.plot_mqq(arm_scale_d={0:0.8,
1:0.7,
2:0.6,
3:0.8},
skip=3,cut=20,anno=True, sig_level_lead=1e-20,mode= "m",check=False,verbose=False)
Out[19]:
(<Figure size 3000x1000 with 1 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
anno_style¶
GWASLab provides three types of different annotation styles
anno_style="right", anno_style="expand", and anno_style="tight"
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mysumstats.plot_mqq(skip=3,cut=20,anno=True,anno_style="expand", sig_level_lead=1e-20,mode= "m",check=False,verbose=False)
mysumstats.plot_mqq(skip=3,cut=20,anno=True,anno_style="expand", sig_level_lead=1e-20,mode= "m",check=False,verbose=False)
Out[20]:
(<Figure size 3000x1000 with 1 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
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mysumstats.plot_mqq(skip=3,cut=20,anno=True,anno_style="tight", sig_level_lead=1e-20,mode= "m", check=False,verbose=False)
mysumstats.plot_mqq(skip=3,cut=20,anno=True,anno_style="tight", sig_level_lead=1e-20,mode= "m", check=False,verbose=False)
Out[21]:
(<Figure size 3000x1000 with 1 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
anno_set¶
If we want to annotate only a subset of variants, we can pass a list of variant IDs to anno_set.
Let's check all lead variants and select only two to annotate.
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mysumstats.get_lead(verbose=False).sort_values(by="P")
mysumstats.get_lead(verbose=False).sort_values(by="P")
Out[22]:
| SNPID | CHR | POS | EA | NEA | EAF | P | STATUS | |
|---|---|---|---|---|---|---|---|---|
| 7947442 | 11:2858546_C_T | 11 | 2858546 | C | T | 0.6209 | 2.580000e-168 | 1995999 |
| 6903480 | 9:22132729_A_G | 9 | 22132729 | G | A | 0.4367 | 9.848000e-88 | 1995999 |
| 4664126 | 6:20688121_T_A | 6 | 20688121 | T | A | 0.5758 | 2.062000e-85 | 1995999 |
| 5965364 | 7:127253550_C_T | 7 | 127253550 | C | T | 0.9081 | 4.101000e-74 | 1995999 |
| 12554976 | X:152908887_G_A | 23 | 152908887 | G | A | 0.6792 | 9.197000e-58 | 1995999 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 12272930 | X:21569920_A_G | 23 | 21569920 | G | A | 0.3190 | 2.616000e-08 | 1995999 |
| 4599424 | 6:7226959_C_T | 6 | 7226959 | C | T | 0.6657 | 2.849000e-08 | 1995999 |
| 10287151 | 15:90393949_C_CT | 15 | 90393949 | C | CT | 0.3445 | 3.134000e-08 | 1995999 |
| 534095 | 1:154309595_TA_T | 1 | 154309595 | TA | T | 0.0947 | 3.289000e-08 | 1995999 |
| 10874150 | 17:40913366_C_T | 17 | 40913366 | C | T | 0.4707 | 4.159000e-08 | 1995999 |
89 rows × 8 columns
This time, let's annotate 1:154309595_TA_T and 2:27734972_G_A with its nearest gene names!
anno_set : the set of variants you want to annotate
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mysumstats.plot_mqq(skip=3,cut=20,anno="GENENAME",anno_set=["1:154309595_TA_T","2:27734972_G_A"],mode= "m",check=False,verbose=False)
mysumstats.plot_mqq(skip=3,cut=20,anno="GENENAME",anno_set=["1:154309595_TA_T","2:27734972_G_A"],mode= "m",check=False,verbose=False)
Out[23]:
(<Figure size 3000x1000 with 1 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
anno_alias¶
anno_alias accepts a dictionary of SNPID:string. You can use this to customized the text for annotation.
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mysumstats.plot_mqq(skip=3,
cut=20,
anno=True,
anno_set=["1:154309595_TA_T","2:27734972_G_A"],
anno_alias={"1:154309595_TA_T":"anything you want here"},
mode= "m",
verbose=False)
mysumstats.plot_mqq(skip=3,
cut=20,
anno=True,
anno_set=["1:154309595_TA_T","2:27734972_G_A"],
anno_alias={"1:154309595_TA_T":"anything you want here"},
mode= "m",
verbose=False)
Out[24]:
(<Figure size 3000x1000 with 1 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
Highlight loci & Pinpoint variants (single group)¶
highlight: a variant list of loci you want to highlightpinpoint: a variant list of variants you want to pinpoint
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mysumstats.plot_mqq(skip=3,cut=20,
anno=True,
anno_set=["2:27734972_G_A","2:27734972_G_A","7:127253550_C_T", "19:46166604_C_T"],
highlight=["19:46166604_C_T","1:154309595_TA_T","7:127253550_C_T"],
highlight_windowkb=1000,
pinpoint=["2:27734972_G_A"],
mode= "m",
check=False,verbose=False)
mysumstats.plot_mqq(skip=3,cut=20,
anno=True,
anno_set=["2:27734972_G_A","2:27734972_G_A","7:127253550_C_T", "19:46166604_C_T"],
highlight=["19:46166604_C_T","1:154309595_TA_T","7:127253550_C_T"],
highlight_windowkb=1000,
pinpoint=["2:27734972_G_A"],
mode= "m",
check=False,verbose=False)
Out[25]:
(<Figure size 3000x1000 with 1 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
Highlight loci & Pinpoint variants (multi-group)¶
Instead of a list, you can provide a list of lists. Each member list is then a group.
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mysumstats.plot_mqq(skip=3,cut=20,
highlight=[
["19:46166604_C_T","1:154309595_TA_T"],
["X:57170781_A_AT","7:127253550_C_T"]
],
highlight_windowkb=1000,
highlight_color=["yellow","red"],
mode= "m",
check=False,verbose=False)
mysumstats.plot_mqq(skip=3,cut=20,
highlight=[
["19:46166604_C_T","1:154309595_TA_T"],
["X:57170781_A_AT","7:127253550_C_T"]
],
highlight_windowkb=1000,
highlight_color=["yellow","red"],
mode= "m",
check=False,verbose=False)
Out[26]:
(<Figure size 3000x1000 with 1 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
MAF-stratified QQ plot¶
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mysumstats.plot_mqq(skip=3,cut=20, mode="mqq",stratified=True,check=False,verbose=False)
mysumstats.plot_mqq(skip=3,cut=20, mode="mqq",stratified=True,check=False,verbose=False)
Out[27]:
(<Figure size 3000x1000 with 2 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
Auxiliary lines¶
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mysumstats.plot_mqq(skip=3,
build="19",
anno="GENENAME",
windowsizekb=1000000,
cut=20,
cut_line_color="purple",
sig_level=5e-8,
sig_level_lead=1e-6,
sig_line_color="grey",
suggestive_sig_line = True,
suggestive_sig_level = 1e-6,
suggestive_sig_line_color="blue",
additional_line=[1e-40,1e-60],
additional_line_color=["yellow","green"],
mode= "m",check=False,verbose=False)
mysumstats.plot_mqq(skip=3,
build="19",
anno="GENENAME",
windowsizekb=1000000,
cut=20,
cut_line_color="purple",
sig_level=5e-8,
sig_level_lead=1e-6,
sig_line_color="grey",
suggestive_sig_line = True,
suggestive_sig_level = 1e-6,
suggestive_sig_line_color="blue",
additional_line=[1e-40,1e-60],
additional_line_color=["yellow","green"],
mode= "m",check=False,verbose=False)
Out[28]:
(<Figure size 3000x1000 with 1 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
Font and marker size¶
fontsizeanno_fontsizetitle_fontsizemarker_size
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mysumstats.plot_mqq(skip=3,
anno="GENENAME",
title= "My Manhattan Plot",
windowsizekb=1000000,
fontsize =13,
anno_fontsize = 15,
title_fontsize = 30,
marker_size=(5,25),
mode= "m",
verbose=False,
check=False
)
mysumstats.plot_mqq(skip=3,
anno="GENENAME",
title= "My Manhattan Plot",
windowsizekb=1000000,
fontsize =13,
anno_fontsize = 15,
title_fontsize = 30,
marker_size=(5,25),
mode= "m",
verbose=False,
check=False
)
Out[29]:
(<Figure size 3000x1000 with 1 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
Colors¶
colorscut_line_colorsig_line_colorhighlight_colorpinpoint_colormaf_bin_colors
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mysumstats.plot_mqq(skip=3,
cut=20,
stratified=True,
highlight=["7:127253550_C_T"],
pinpoint=["2:27734972_G_A"],
colors=["orange","blue"],
cut_line_color="yellow",
sig_line_color="red",
highlight_color="purple",
pinpoint_color ="green",
maf_bin_colors = ["#FFE2D1","#E1F0C4", "#6BAB90","#55917F"],
check=False,verbose=False
)
mysumstats.plot_mqq(skip=3,
cut=20,
stratified=True,
highlight=["7:127253550_C_T"],
pinpoint=["2:27734972_G_A"],
colors=["orange","blue"],
cut_line_color="yellow",
sig_line_color="red",
highlight_color="purple",
pinpoint_color ="green",
maf_bin_colors = ["#FFE2D1","#E1F0C4", "#6BAB90","#55917F"],
check=False,verbose=False
)
Out[30]:
(<Figure size 3000x1000 with 2 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
Save plots¶
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mysumstats.plot_mqq(skip=3,
cut=20,
mode="mqq",
stratified=True,
save="my_maf_stratified_mqq_plot.png",
save_args={"dpi":300,"facecolor":"white"})
mysumstats.plot_mqq(skip=3,
cut=20,
mode="mqq",
stratified=True,
save="my_maf_stratified_mqq_plot.png",
save_args={"dpi":300,"facecolor":"white"})
2024/10/29 17:32:02 Start to create MQQ plot...v3.5.0: 2024/10/29 17:32:02 -Genomic coordinates version: 19... 2024/10/29 17:32:02 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:32:02 -Raw input contains 12557761 variants... 2024/10/29 17:32:02 -MQQ plot layout mode is : mqq 2024/10/29 17:32:04 Finished loading specified columns from the sumstats. 2024/10/29 17:32:04 Start data conversion and sanity check: 2024/10/29 17:32:04 -Removed 0 variants with nan in CHR or POS column ... 2024/10/29 17:32:06 -Removed 0 variants with CHR <=0... 2024/10/29 17:32:07 -Removed 0 variants with nan in EAF column ... 2024/10/29 17:32:07 -Removed 0 variants with nan in P column ... 2024/10/29 17:32:07 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:32:08 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:32:08 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:32:09 -Converting data above cut line... 2024/10/29 17:32:09 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:32:09 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:32:09 Finished data conversion and sanity check. 2024/10/29 17:32:09 Start to create MQQ plot with 91234 variants... 2024/10/29 17:32:09 -Creating background plot... 2024/10/29 17:32:09 Finished creating MQQ plot successfully! 2024/10/29 17:32:09 Start to extract variants for annotation... 2024/10/29 17:32:10 -Found 89 significant variants with a sliding window size of 500 kb... 2024/10/29 17:32:10 Finished extracting variants for annotation... 2024/10/29 17:32:10 Start to process figure arts. 2024/10/29 17:32:10 -Processing X ticks... 2024/10/29 17:32:10 -Processing X labels... 2024/10/29 17:32:10 -Processing Y labels... 2024/10/29 17:32:10 -Processing Y tick lables... 2024/10/29 17:32:10 -Processing Y labels... 2024/10/29 17:32:10 -Processing lines... 2024/10/29 17:32:10 Finished processing figure arts. 2024/10/29 17:32:10 Start to annotate variants... 2024/10/29 17:32:10 -Skip annotating 2024/10/29 17:32:10 Finished annotating variants. 2024/10/29 17:32:10 Start to create QQ plot with 91234 variants: 2024/10/29 17:32:10 -Plotting variants stratified by MAF... 2024/10/29 17:32:11 -Lambda GC (MLOG10P mode) at 0.5 is 1.21283 2024/10/29 17:32:11 -Processing Y tick lables... 2024/10/29 17:32:11 Finished creating QQ plot successfully! 2024/10/29 17:32:11 Start to save figure... 2024/10/29 17:32:12 -Saved to my_maf_stratified_mqq_plot.png successfully! (overwrite) 2024/10/29 17:32:12 Finished saving figure... 2024/10/29 17:32:12 Finished creating plot successfully!
Out[31]:
(<Figure size 4500x1500 with 2 Axes>, <gwaslab.g_Log.Log at 0x7f781811d0a0>)
Fig and Log object¶
plot_mqq will return a matplotlib figure object and a gwaslab log object
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my_mqqplot,my_log = mysumstats.plot_mqq(skip=3,cut=20, mode="mqq",stratified=True,verbose=False)
my_mqqplot,my_log = mysumstats.plot_mqq(skip=3,cut=20, mode="mqq",stratified=True,verbose=False)
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my_mqqplot
my_mqqplot
Out[33]:
In [34]:
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my_log
my_log
Out[34]:
<gwaslab.g_Log.Log at 0x7f781811d0a0>
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my_log.show()
my_log.show()
2024/10/29 17:25:09 Sumstats Object created. 2024/10/29 17:25:41 Start to create MQQ plot...v3.5.0: 2024/10/29 17:25:41 -Genomic coordinates version: 19... 2024/10/29 17:25:41 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:25:41 -Raw input contains 12557761 variants... 2024/10/29 17:25:41 -MQQ plot layout mode is : mqq 2024/10/29 17:25:42 Finished loading specified columns from the sumstats. 2024/10/29 17:25:42 Start data conversion and sanity check: 2024/10/29 17:25:43 -Removed 0 variants with nan in CHR or POS column ... 2024/10/29 17:25:44 -Removed 0 variants with CHR <=0... 2024/10/29 17:25:45 -Removed 0 variants with nan in P column ... 2024/10/29 17:25:45 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:25:45 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:25:46 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:25:47 -Converting data above cut line... 2024/10/29 17:25:47 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:25:47 Finished data conversion and sanity check. 2024/10/29 17:25:47 Start to create MQQ plot with 12557761 variants... 2024/10/29 17:26:00 -Creating background plot... 2024/10/29 17:26:19 Finished creating MQQ plot successfully! 2024/10/29 17:26:19 Start to extract variants for annotation... 2024/10/29 17:26:20 -Found 89 significant variants with a sliding window size of 500 kb... 2024/10/29 17:26:20 Finished extracting variants for annotation... 2024/10/29 17:26:20 Start to process figure arts. 2024/10/29 17:26:20 -Processing X ticks... 2024/10/29 17:26:20 -Processing X labels... 2024/10/29 17:26:20 -Processing Y labels... 2024/10/29 17:26:20 -Processing Y tick lables... 2024/10/29 17:26:20 -Processing Y labels... 2024/10/29 17:26:20 -Processing lines... 2024/10/29 17:26:20 Finished processing figure arts. 2024/10/29 17:26:20 Start to annotate variants... 2024/10/29 17:26:20 -Skip annotating 2024/10/29 17:26:20 Finished annotating variants. 2024/10/29 17:26:20 Start to create QQ plot with 12557761 variants: 2024/10/29 17:26:20 -Plotting all variants... 2024/10/29 17:26:21 -Expected range of P: (0,1.0) 2024/10/29 17:26:22 -Lambda GC (MLOG10P mode) at 0.5 is 1.21283 2024/10/29 17:26:22 -Processing Y tick lables... 2024/10/29 17:26:22 Finished creating QQ plot successfully! 2024/10/29 17:26:22 Start to save figure... 2024/10/29 17:26:22 -Skip saving figure! 2024/10/29 17:26:22 Finished saving figure... 2024/10/29 17:26:22 Finished creating plot successfully! 2024/10/29 17:27:47 Start to create MQQ plot...v3.5.0: 2024/10/29 17:27:47 -Genomic coordinates version: 19... 2024/10/29 17:27:47 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:27:47 -Raw input contains 12557761 variants... 2024/10/29 17:27:47 -MQQ plot layout mode is : qqm 2024/10/29 17:27:48 Finished loading specified columns from the sumstats. 2024/10/29 17:27:48 Start data conversion and sanity check: 2024/10/29 17:27:48 -Sanity check will be skipped. 2024/10/29 17:27:49 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:27:49 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:27:50 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:27:51 -Converting data above cut line... 2024/10/29 17:27:51 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:27:51 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:27:51 Finished data conversion and sanity check. 2024/10/29 17:27:51 Start to create MQQ plot with 91234 variants... 2024/10/29 17:27:51 -Creating background plot... 2024/10/29 17:27:51 Finished creating MQQ plot successfully! 2024/10/29 17:27:51 Start to extract variants for annotation... 2024/10/29 17:27:51 -Found 89 significant variants with a sliding window size of 500 kb... 2024/10/29 17:27:51 Finished extracting variants for annotation... 2024/10/29 17:27:51 Start to process figure arts. 2024/10/29 17:27:51 -Processing X ticks... 2024/10/29 17:27:51 -Processing X labels... 2024/10/29 17:27:51 -Processing Y labels... 2024/10/29 17:27:51 -Processing Y tick lables... 2024/10/29 17:27:51 -Processing Y labels... 2024/10/29 17:27:51 -Processing lines... 2024/10/29 17:27:51 Finished processing figure arts. 2024/10/29 17:27:51 Start to annotate variants... 2024/10/29 17:27:51 -Skip annotating 2024/10/29 17:27:51 Finished annotating variants. 2024/10/29 17:27:51 Start to create QQ plot with 91234 variants: 2024/10/29 17:27:51 -Plotting all variants... 2024/10/29 17:27:51 -Expected range of P: (0,1.0) 2024/10/29 17:27:52 -Lambda GC (MLOG10P mode) at 0.5 is 1.21283 2024/10/29 17:27:52 -Processing Y tick lables... 2024/10/29 17:27:52 Finished creating QQ plot successfully! 2024/10/29 17:27:52 Start to save figure... 2024/10/29 17:27:52 -Skip saving figure! 2024/10/29 17:27:52 Finished saving figure... 2024/10/29 17:27:52 Finished creating plot successfully! 2024/10/29 17:27:53 Start to create MQQ plot...v3.5.0: 2024/10/29 17:27:53 -Genomic coordinates version: 19... 2024/10/29 17:27:53 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:27:53 -Raw input contains 12557761 variants... 2024/10/29 17:27:53 -MQQ plot layout mode is : m 2024/10/29 17:27:54 Finished loading specified columns from the sumstats. 2024/10/29 17:27:54 Start data conversion and sanity check: 2024/10/29 17:27:54 -Sanity check will be skipped. 2024/10/29 17:27:54 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:27:55 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:27:55 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:27:56 -Converting data above cut line... 2024/10/29 17:27:56 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:27:56 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:27:56 Finished data conversion and sanity check. 2024/10/29 17:27:56 Start to create MQQ plot with 91234 variants... 2024/10/29 17:27:56 -Creating background plot... 2024/10/29 17:27:56 Finished creating MQQ plot successfully! 2024/10/29 17:27:56 Start to extract variants for annotation... 2024/10/29 17:27:57 -Found 89 significant variants with a sliding window size of 500 kb... 2024/10/29 17:27:57 Finished extracting variants for annotation... 2024/10/29 17:27:57 Start to process figure arts. 2024/10/29 17:27:57 -Processing X ticks... 2024/10/29 17:27:57 -Processing X labels... 2024/10/29 17:27:57 -Processing Y labels... 2024/10/29 17:27:57 -Processing Y tick lables... 2024/10/29 17:27:57 -Processing Y labels... 2024/10/29 17:27:57 -Processing lines... 2024/10/29 17:27:57 Finished processing figure arts. 2024/10/29 17:27:57 Start to annotate variants... 2024/10/29 17:27:57 -Skip annotating 2024/10/29 17:27:57 Finished annotating variants. 2024/10/29 17:27:57 Start to save figure... 2024/10/29 17:27:57 -Skip saving figure! 2024/10/29 17:27:57 Finished saving figure... 2024/10/29 17:27:57 Finished creating plot successfully! 2024/10/29 17:27:57 Start to create MQQ plot...v3.5.0: 2024/10/29 17:27:57 -Genomic coordinates version: 19... 2024/10/29 17:27:57 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:27:57 -Raw input contains 12557761 variants... 2024/10/29 17:27:57 -MQQ plot layout mode is : qq 2024/10/29 17:27:58 Finished loading specified columns from the sumstats. 2024/10/29 17:27:58 Start data conversion and sanity check: 2024/10/29 17:27:58 -Sanity check will be skipped. 2024/10/29 17:27:58 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:27:59 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:27:59 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:28:00 -Converting data above cut line... 2024/10/29 17:28:00 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:28:00 Finished data conversion and sanity check. 2024/10/29 17:28:00 Start to create MQQ plot with 12557761 variants... 2024/10/29 17:28:00 Start to create QQ plot with 12557761 variants: 2024/10/29 17:28:00 -Plotting all variants... 2024/10/29 17:28:02 -Expected range of P: (0,1.0) 2024/10/29 17:28:03 -Lambda GC (MLOG10P mode) at 0.5 is 1.21283 2024/10/29 17:28:03 -Processing Y tick lables... 2024/10/29 17:28:03 Finished creating QQ plot successfully! 2024/10/29 17:28:03 Start to save figure... 2024/10/29 17:28:03 -Skip saving figure! 2024/10/29 17:28:03 Finished saving figure... 2024/10/29 17:28:03 Finished creating plot successfully! 2024/10/29 17:28:32 Start to create MQQ plot...v3.5.0: 2024/10/29 17:28:32 -Genomic coordinates version: 19... 2024/10/29 17:28:32 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:28:32 -Raw input contains 12557761 variants... 2024/10/29 17:28:32 -MQQ plot layout mode is : m 2024/10/29 17:28:33 Finished loading specified columns from the sumstats. 2024/10/29 17:28:33 Start data conversion and sanity check: 2024/10/29 17:28:33 -Sanity check will be skipped. 2024/10/29 17:28:34 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:28:34 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:28:35 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:28:36 -Converting data above cut line... 2024/10/29 17:28:36 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:28:36 Finished data conversion and sanity check. 2024/10/29 17:28:36 Start to create MQQ plot with 21766 variants... 2024/10/29 17:28:36 -Creating background plot... 2024/10/29 17:28:36 Finished creating MQQ plot successfully! 2024/10/29 17:28:36 Start to extract variants for annotation... 2024/10/29 17:28:36 -Found 89 significant variants with a sliding window size of 500 kb... 2024/10/29 17:28:36 Finished extracting variants for annotation... 2024/10/29 17:28:36 Start to process figure arts. 2024/10/29 17:28:36 -Processing X ticks... 2024/10/29 17:28:36 -Processing X labels... 2024/10/29 17:28:36 -Processing Y labels... 2024/10/29 17:28:36 -Processing Y tick lables... 2024/10/29 17:28:36 -Processing Y labels... 2024/10/29 17:28:36 -Processing lines... 2024/10/29 17:28:36 Finished processing figure arts. 2024/10/29 17:28:36 Start to annotate variants... 2024/10/29 17:28:36 -Skip annotating 2024/10/29 17:28:36 Finished annotating variants. 2024/10/29 17:28:36 Start to save figure... 2024/10/29 17:28:36 -Skip saving figure! 2024/10/29 17:28:36 Finished saving figure... 2024/10/29 17:28:36 Finished creating plot successfully! 2024/10/29 17:28:36 Start to create MQQ plot...v3.5.0: 2024/10/29 17:28:36 -Genomic coordinates version: 19... 2024/10/29 17:28:36 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:28:36 -Raw input contains 12557761 variants... 2024/10/29 17:28:36 -MQQ plot layout mode is : m 2024/10/29 17:28:37 Finished loading specified columns from the sumstats. 2024/10/29 17:28:37 Start data conversion and sanity check: 2024/10/29 17:28:37 -Sanity check will be skipped. 2024/10/29 17:28:38 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:28:38 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:28:39 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:28:40 -Converting data above cut line... 2024/10/29 17:28:40 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:28:40 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:28:40 Finished data conversion and sanity check. 2024/10/29 17:28:40 Start to create MQQ plot with 12557761 variants... 2024/10/29 17:28:53 -Creating background plot... 2024/10/29 17:29:12 Finished creating MQQ plot successfully! 2024/10/29 17:29:12 Start to extract variants for annotation... 2024/10/29 17:29:12 -Found 89 significant variants with a sliding window size of 500 kb... 2024/10/29 17:29:12 Finished extracting variants for annotation... 2024/10/29 17:29:12 Start to process figure arts. 2024/10/29 17:29:12 -Processing X ticks... 2024/10/29 17:29:12 -Processing X labels... 2024/10/29 17:29:12 -Processing Y labels... 2024/10/29 17:29:12 -Processing Y tick lables... 2024/10/29 17:29:12 -Processing Y labels... 2024/10/29 17:29:12 -Processing lines... 2024/10/29 17:29:12 Finished processing figure arts. 2024/10/29 17:29:12 Start to annotate variants... 2024/10/29 17:29:12 -Skip annotating 2024/10/29 17:29:12 Finished annotating variants. 2024/10/29 17:29:12 Start to save figure... 2024/10/29 17:29:12 -Skip saving figure! 2024/10/29 17:29:12 Finished saving figure... 2024/10/29 17:29:13 Finished creating plot successfully! 2024/10/29 17:30:09 Start to create MQQ plot...v3.5.0: 2024/10/29 17:30:09 -Genomic coordinates version: 19... 2024/10/29 17:30:09 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:30:09 -Raw input contains 12557761 variants... 2024/10/29 17:30:09 -MQQ plot layout mode is : m 2024/10/29 17:30:10 Finished loading specified columns from the sumstats. 2024/10/29 17:30:10 Start data conversion and sanity check: 2024/10/29 17:30:10 -Sanity check will be skipped. 2024/10/29 17:30:10 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:30:11 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:30:11 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:30:12 -Converting data above cut line... 2024/10/29 17:30:12 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:30:12 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:30:12 Finished data conversion and sanity check. 2024/10/29 17:30:12 Start to create MQQ plot with 91234 variants... 2024/10/29 17:30:12 -Creating background plot... 2024/10/29 17:30:12 Finished creating MQQ plot successfully! 2024/10/29 17:30:12 Start to extract variants for annotation... 2024/10/29 17:30:13 -Found 89 significant variants with a sliding window size of 500 kb... 2024/10/29 17:30:13 Finished extracting variants for annotation... 2024/10/29 17:30:13 Start to process figure arts. 2024/10/29 17:30:13 -Processing X ticks... 2024/10/29 17:30:13 -Processing X labels... 2024/10/29 17:30:13 -Processing Y labels... 2024/10/29 17:30:13 -Processing Y tick lables... 2024/10/29 17:30:13 -Processing Y labels... 2024/10/29 17:30:13 -Processing lines... 2024/10/29 17:30:13 Finished processing figure arts. 2024/10/29 17:30:13 Start to annotate variants... 2024/10/29 17:30:13 -Skip annotating 2024/10/29 17:30:13 Finished annotating variants. 2024/10/29 17:30:13 -Processing jagged Y axis... 2024/10/29 17:30:13 Start to save figure... 2024/10/29 17:30:13 -Skip saving figure! 2024/10/29 17:30:13 Finished saving figure... 2024/10/29 17:30:13 Finished creating plot successfully! 2024/10/29 17:30:13 Start to create MQQ plot...v3.5.0: 2024/10/29 17:30:13 -Genomic coordinates version: 19... 2024/10/29 17:30:13 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:30:13 -Raw input contains 12557761 variants... 2024/10/29 17:30:13 -MQQ plot layout mode is : m 2024/10/29 17:30:14 Finished loading specified columns from the sumstats. 2024/10/29 17:30:14 Start data conversion and sanity check: 2024/10/29 17:30:14 -Sanity check will be skipped. 2024/10/29 17:30:15 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:30:15 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:30:16 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:30:17 -Converting data above cut line... 2024/10/29 17:30:17 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:30:17 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:30:17 Finished data conversion and sanity check. 2024/10/29 17:30:17 Start to create MQQ plot with 91234 variants... 2024/10/29 17:30:17 -Creating background plot... 2024/10/29 17:30:17 Finished creating MQQ plot successfully! 2024/10/29 17:30:17 Start to extract variants for annotation... 2024/10/29 17:30:17 -Found 89 significant variants with a sliding window size of 500 kb... 2024/10/29 17:30:17 Finished extracting variants for annotation... 2024/10/29 17:30:17 Start to process figure arts. 2024/10/29 17:30:17 -Processing X ticks... 2024/10/29 17:30:17 -Processing X labels... 2024/10/29 17:30:17 -Processing Y labels... 2024/10/29 17:30:17 -Processing Y tick lables... 2024/10/29 17:30:17 -Processing Y labels... 2024/10/29 17:30:17 -Processing lines... 2024/10/29 17:30:17 Finished processing figure arts. 2024/10/29 17:30:17 Start to annotate variants... 2024/10/29 17:30:17 -Skip annotating 2024/10/29 17:30:17 Finished annotating variants. 2024/10/29 17:30:17 Start to save figure... 2024/10/29 17:30:17 -Skip saving figure! 2024/10/29 17:30:17 Finished saving figure... 2024/10/29 17:30:17 Finished creating plot successfully! 2024/10/29 17:30:18 Start to create MQQ plot...v3.5.0: 2024/10/29 17:30:18 -Genomic coordinates version: 19... 2024/10/29 17:30:18 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:30:18 -Raw input contains 12557761 variants... 2024/10/29 17:30:18 -MQQ plot layout mode is : m 2024/10/29 17:30:19 Finished loading specified columns from the sumstats. 2024/10/29 17:30:19 Start data conversion and sanity check: 2024/10/29 17:30:19 -Sanity check will be skipped. 2024/10/29 17:30:19 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:30:20 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:30:20 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:30:21 -Converting data above cut line... 2024/10/29 17:30:21 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:30:21 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:30:21 Finished data conversion and sanity check. 2024/10/29 17:30:21 Start to create MQQ plot with 91234 variants... 2024/10/29 17:30:21 -Creating background plot... 2024/10/29 17:30:21 Finished creating MQQ plot successfully! 2024/10/29 17:30:21 Start to extract variants for annotation... 2024/10/29 17:30:22 -Found 89 significant variants with a sliding window size of 500 kb... 2024/10/29 17:30:22 Finished extracting variants for annotation... 2024/10/29 17:30:22 Start to process figure arts. 2024/10/29 17:30:22 -Processing X ticks... 2024/10/29 17:30:22 -Processing X labels... 2024/10/29 17:30:22 -Processing Y labels... 2024/10/29 17:30:22 -Processing Y tick lables... 2024/10/29 17:30:22 -Processing Y labels... 2024/10/29 17:30:22 -Processing lines... 2024/10/29 17:30:22 Finished processing figure arts. 2024/10/29 17:30:22 Start to annotate variants... 2024/10/29 17:30:22 -Skip annotating 2024/10/29 17:30:22 Finished annotating variants. 2024/10/29 17:30:22 -Adjusting X padding on both side : tight mode 2024/10/29 17:30:22 Start to save figure... 2024/10/29 17:30:22 -Skip saving figure! 2024/10/29 17:30:22 Finished saving figure... 2024/10/29 17:30:22 Finished creating plot successfully! 2024/10/29 17:30:23 Start to create MQQ plot...v3.5.0: 2024/10/29 17:30:23 -Genomic coordinates version: 19... 2024/10/29 17:30:23 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:30:23 -Raw input contains 12557761 variants... 2024/10/29 17:30:23 -MQQ plot layout mode is : m 2024/10/29 17:30:24 Finished loading specified columns from the sumstats. 2024/10/29 17:30:24 Start data conversion and sanity check: 2024/10/29 17:30:24 -Sanity check will be skipped. 2024/10/29 17:30:24 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:30:24 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:30:25 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:30:26 -Converting data above cut line... 2024/10/29 17:30:26 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:30:26 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:30:26 Finished data conversion and sanity check. 2024/10/29 17:30:26 Start to create MQQ plot with 91234 variants... 2024/10/29 17:30:26 -Creating background plot... 2024/10/29 17:30:26 Finished creating MQQ plot successfully! 2024/10/29 17:30:26 Start to extract variants for annotation... 2024/10/29 17:30:26 -Found 89 significant variants with a sliding window size of 500 kb... 2024/10/29 17:30:26 Finished extracting variants for annotation... 2024/10/29 17:30:26 Start to process figure arts. 2024/10/29 17:30:26 -Processing X ticks... 2024/10/29 17:30:26 -Processing X labels... 2024/10/29 17:30:26 -Processing Y labels... 2024/10/29 17:30:26 -Processing Y tick lables... 2024/10/29 17:30:26 -Processing Y labels... 2024/10/29 17:30:26 -Processing lines... 2024/10/29 17:30:26 Finished processing figure arts. 2024/10/29 17:30:26 Start to annotate variants... 2024/10/29 17:30:26 -Skip annotating 2024/10/29 17:30:26 Finished annotating variants. 2024/10/29 17:30:26 -Adjusting X padding on both side : tight mode 2024/10/29 17:30:26 Start to save figure... 2024/10/29 17:30:26 -Skip saving figure! 2024/10/29 17:30:26 Finished saving figure... 2024/10/29 17:30:26 Finished creating plot successfully! 2024/10/29 17:30:27 Start to create MQQ plot...v3.5.0: 2024/10/29 17:30:27 -Genomic coordinates version: 19... 2024/10/29 17:30:27 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:30:27 -Raw input contains 12557761 variants... 2024/10/29 17:30:27 -MQQ plot layout mode is : m 2024/10/29 17:30:28 Finished loading specified columns from the sumstats. 2024/10/29 17:30:28 Start data conversion and sanity check: 2024/10/29 17:30:28 -Sanity check will be skipped. 2024/10/29 17:30:29 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:30:29 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:30:29 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:30:30 -Converting data above cut line... 2024/10/29 17:30:30 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:30:30 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:30:30 Finished data conversion and sanity check. 2024/10/29 17:30:30 Start to create MQQ plot with 91234 variants... 2024/10/29 17:30:30 -Creating background plot... 2024/10/29 17:30:31 Finished creating MQQ plot successfully! 2024/10/29 17:30:31 Start to extract variants for annotation... 2024/10/29 17:30:31 -Found 89 significant variants with a sliding window size of 500 kb... 2024/10/29 17:30:31 Finished extracting variants for annotation... 2024/10/29 17:30:31 Start to process figure arts. 2024/10/29 17:30:31 -Processing X ticks... 2024/10/29 17:30:31 -Processing X labels... 2024/10/29 17:30:31 -Processing Y labels... 2024/10/29 17:30:31 -Processing Y tick lables... 2024/10/29 17:30:31 -Processing Y labels... 2024/10/29 17:30:31 -Processing lines... 2024/10/29 17:30:31 Finished processing figure arts. 2024/10/29 17:30:31 Start to annotate variants... 2024/10/29 17:30:31 -Annotating using column CHR:POS... 2024/10/29 17:30:31 -Adjusting text positions with repel_force=0.03... 2024/10/29 17:30:31 Finished annotating variants. 2024/10/29 17:30:31 Start to save figure... 2024/10/29 17:30:31 -Skip saving figure! 2024/10/29 17:30:31 Finished saving figure... 2024/10/29 17:30:31 Finished creating plot successfully! 2024/10/29 17:30:33 Start to create MQQ plot...v3.5.0: 2024/10/29 17:30:33 -Genomic coordinates version: 19... 2024/10/29 17:30:33 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:30:33 -Raw input contains 12557761 variants... 2024/10/29 17:30:33 -MQQ plot layout mode is : m 2024/10/29 17:30:34 Finished loading specified columns from the sumstats. 2024/10/29 17:30:34 Start data conversion and sanity check: 2024/10/29 17:30:34 -Sanity check will be skipped. 2024/10/29 17:30:35 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:30:35 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:30:36 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:30:37 -Converting data above cut line... 2024/10/29 17:30:37 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:30:37 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:30:37 Finished data conversion and sanity check. 2024/10/29 17:30:37 Start to create MQQ plot with 91234 variants... 2024/10/29 17:30:37 -Creating background plot... 2024/10/29 17:30:37 Finished creating MQQ plot successfully! 2024/10/29 17:30:37 Start to extract variants for annotation... 2024/10/29 17:30:37 -Found 16 significant variants with a sliding window size of 500 kb... 2024/10/29 17:30:37 Finished extracting variants for annotation... 2024/10/29 17:30:37 Start to process figure arts. 2024/10/29 17:30:37 -Processing X ticks... 2024/10/29 17:30:37 -Processing X labels... 2024/10/29 17:30:37 -Processing Y labels... 2024/10/29 17:30:37 -Processing Y tick lables... 2024/10/29 17:30:37 -Processing Y labels... 2024/10/29 17:30:37 -Processing lines... 2024/10/29 17:30:37 Finished processing figure arts. 2024/10/29 17:30:37 Start to annotate variants... 2024/10/29 17:30:37 -Annotating using column CHR:POS... 2024/10/29 17:30:37 -Adjusting text positions with repel_force=0.03... 2024/10/29 17:30:37 Finished annotating variants. 2024/10/29 17:30:37 Start to save figure... 2024/10/29 17:30:37 -Skip saving figure! 2024/10/29 17:30:37 Finished saving figure... 2024/10/29 17:30:37 Finished creating plot successfully! 2024/10/29 17:30:38 Start to create MQQ plot...v3.5.0: 2024/10/29 17:30:38 -Genomic coordinates version: 19... 2024/10/29 17:30:38 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:30:38 -Raw input contains 12557761 variants... 2024/10/29 17:30:38 -MQQ plot layout mode is : m 2024/10/29 17:30:39 Finished loading specified columns from the sumstats. 2024/10/29 17:30:39 Start data conversion and sanity check: 2024/10/29 17:30:39 -Sanity check will be skipped. 2024/10/29 17:30:39 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:30:40 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:30:40 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:30:41 -Converting data above cut line... 2024/10/29 17:30:41 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:30:41 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:30:41 Finished data conversion and sanity check. 2024/10/29 17:30:41 Start to create MQQ plot with 91234 variants... 2024/10/29 17:30:41 -Creating background plot... 2024/10/29 17:30:42 Finished creating MQQ plot successfully! 2024/10/29 17:30:42 Start to extract variants for annotation... 2024/10/29 17:30:42 -Found 16 significant variants with a sliding window size of 500 kb... 2024/10/29 17:30:42 Start to annotate variants with nearest gene name(s)... 2024/10/29 17:30:42 -Assigning Gene name using ensembl_hg19_gtf for protein coding genes 2024/10/29 17:30:42 Finished annotating variants with nearest gene name(s) successfully! 2024/10/29 17:30:42 Finished extracting variants for annotation... 2024/10/29 17:30:42 Start to process figure arts. 2024/10/29 17:30:42 -Processing X ticks... 2024/10/29 17:30:42 -Processing X labels... 2024/10/29 17:30:42 -Processing Y labels... 2024/10/29 17:30:42 -Processing Y tick lables... 2024/10/29 17:30:42 -Processing Y labels... 2024/10/29 17:30:42 -Processing lines... 2024/10/29 17:30:42 Finished processing figure arts. 2024/10/29 17:30:42 Start to annotate variants... 2024/10/29 17:30:42 -Annotating using column GENENAME... 2024/10/29 17:30:42 -Adjusting text positions with repel_force=0.03... 2024/10/29 17:30:42 Finished annotating variants. 2024/10/29 17:30:42 Start to save figure... 2024/10/29 17:30:42 -Skip saving figure! 2024/10/29 17:30:42 Finished saving figure... 2024/10/29 17:30:42 Finished creating plot successfully! 2024/10/29 17:30:43 Start to create MQQ plot...v3.5.0: 2024/10/29 17:30:43 -Genomic coordinates version: 19... 2024/10/29 17:30:43 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:30:43 -Raw input contains 12557761 variants... 2024/10/29 17:30:43 -MQQ plot layout mode is : m 2024/10/29 17:30:44 Finished loading specified columns from the sumstats. 2024/10/29 17:30:44 Start data conversion and sanity check: 2024/10/29 17:30:44 -Sanity check will be skipped. 2024/10/29 17:30:44 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:30:45 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:30:45 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:30:46 -Converting data above cut line... 2024/10/29 17:30:46 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:30:46 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:30:46 Finished data conversion and sanity check. 2024/10/29 17:30:46 Start to create MQQ plot with 91234 variants... 2024/10/29 17:30:46 -Creating background plot... 2024/10/29 17:30:46 Finished creating MQQ plot successfully! 2024/10/29 17:30:46 Start to extract variants for annotation... 2024/10/29 17:30:47 -Found 16 significant variants with a sliding window size of 500 kb... 2024/10/29 17:30:47 Finished extracting variants for annotation... 2024/10/29 17:30:47 Start to process figure arts. 2024/10/29 17:30:47 -Processing X ticks... 2024/10/29 17:30:47 -Processing X labels... 2024/10/29 17:30:47 -Processing Y labels... 2024/10/29 17:30:47 -Processing Y tick lables... 2024/10/29 17:30:47 -Processing Y labels... 2024/10/29 17:30:47 -Processing lines... 2024/10/29 17:30:47 Finished processing figure arts. 2024/10/29 17:30:47 Start to annotate variants... 2024/10/29 17:30:47 -Annotating using column CHR:POS... 2024/10/29 17:30:47 -Adjusting text positions with repel_force=0.03... 2024/10/29 17:30:47 Finished annotating variants. 2024/10/29 17:30:47 Start to save figure... 2024/10/29 17:30:47 -Skip saving figure! 2024/10/29 17:30:47 Finished saving figure... 2024/10/29 17:30:47 Finished creating plot successfully! 2024/10/29 17:30:48 Start to create MQQ plot...v3.5.0: 2024/10/29 17:30:48 -Genomic coordinates version: 19... 2024/10/29 17:30:48 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:30:48 -Raw input contains 12557761 variants... 2024/10/29 17:30:48 -MQQ plot layout mode is : m 2024/10/29 17:30:49 Finished loading specified columns from the sumstats. 2024/10/29 17:30:49 Start data conversion and sanity check: 2024/10/29 17:30:49 -Sanity check will be skipped. 2024/10/29 17:30:49 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:30:50 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:30:50 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:30:51 -Converting data above cut line... 2024/10/29 17:30:51 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:30:51 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:30:51 Finished data conversion and sanity check. 2024/10/29 17:30:51 Start to create MQQ plot with 91234 variants... 2024/10/29 17:30:51 -Creating background plot... 2024/10/29 17:30:51 Finished creating MQQ plot successfully! 2024/10/29 17:30:51 Start to extract variants for annotation... 2024/10/29 17:30:51 -Found 16 significant variants with a sliding window size of 500 kb... 2024/10/29 17:30:51 Finished extracting variants for annotation... 2024/10/29 17:30:51 Start to process figure arts. 2024/10/29 17:30:51 -Processing X ticks... 2024/10/29 17:30:51 -Processing X labels... 2024/10/29 17:30:51 -Processing Y labels... 2024/10/29 17:30:51 -Processing Y tick lables... 2024/10/29 17:30:51 -Processing Y labels... 2024/10/29 17:30:51 -Processing lines... 2024/10/29 17:30:51 Finished processing figure arts. 2024/10/29 17:30:51 Start to annotate variants... 2024/10/29 17:30:51 -Annotating using column CHR:POS... 2024/10/29 17:30:51 -Adjusting text positions with repel_force=0.03... 2024/10/29 17:30:51 Finished annotating variants. 2024/10/29 17:30:51 Start to save figure... 2024/10/29 17:30:51 -Skip saving figure! 2024/10/29 17:30:51 Finished saving figure... 2024/10/29 17:30:52 Finished creating plot successfully! 2024/10/29 17:30:53 Start to create MQQ plot...v3.5.0: 2024/10/29 17:30:53 -Genomic coordinates version: 19... 2024/10/29 17:30:53 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:30:53 -Raw input contains 12557761 variants... 2024/10/29 17:30:53 -MQQ plot layout mode is : m 2024/10/29 17:30:53 Finished loading specified columns from the sumstats. 2024/10/29 17:30:53 Start data conversion and sanity check: 2024/10/29 17:30:53 -Sanity check will be skipped. 2024/10/29 17:30:54 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:30:54 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:30:55 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:30:56 -Converting data above cut line... 2024/10/29 17:30:56 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:30:56 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:30:56 Finished data conversion and sanity check. 2024/10/29 17:30:56 Start to create MQQ plot with 91234 variants... 2024/10/29 17:30:56 -Creating background plot... 2024/10/29 17:30:56 Finished creating MQQ plot successfully! 2024/10/29 17:30:56 Start to extract variants for annotation... 2024/10/29 17:30:56 -Found 16 significant variants with a sliding window size of 500 kb... 2024/10/29 17:30:56 Finished extracting variants for annotation... 2024/10/29 17:30:56 Start to process figure arts. 2024/10/29 17:30:56 -Processing X ticks... 2024/10/29 17:30:56 -Processing X labels... 2024/10/29 17:30:56 -Processing Y labels... 2024/10/29 17:30:56 -Processing Y tick lables... 2024/10/29 17:30:56 -Processing Y labels... 2024/10/29 17:30:56 -Processing lines... 2024/10/29 17:30:56 Finished processing figure arts. 2024/10/29 17:30:56 Start to annotate variants... 2024/10/29 17:30:56 -Annotating using column CHR:POS... 2024/10/29 17:30:56 -Adjusting text positions with repel_force=0.03... 2024/10/29 17:30:56 Finished annotating variants. 2024/10/29 17:30:56 Start to save figure... 2024/10/29 17:30:56 -Skip saving figure! 2024/10/29 17:30:56 Finished saving figure... 2024/10/29 17:30:56 Finished creating plot successfully! 2024/10/29 17:30:57 Start to create MQQ plot...v3.5.0: 2024/10/29 17:30:57 -Genomic coordinates version: 19... 2024/10/29 17:30:57 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:30:57 -Raw input contains 12557761 variants... 2024/10/29 17:30:57 -MQQ plot layout mode is : m 2024/10/29 17:30:58 Finished loading specified columns from the sumstats. 2024/10/29 17:30:58 Start data conversion and sanity check: 2024/10/29 17:30:58 -Sanity check will be skipped. 2024/10/29 17:30:58 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:30:59 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:30:59 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:31:00 -Converting data above cut line... 2024/10/29 17:31:00 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:31:00 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:31:00 Finished data conversion and sanity check. 2024/10/29 17:31:00 Start to create MQQ plot with 91234 variants... 2024/10/29 17:31:00 -Creating background plot... 2024/10/29 17:31:00 Finished creating MQQ plot successfully! 2024/10/29 17:31:00 Start to extract variants for annotation... 2024/10/29 17:31:01 -Found 16 significant variants with a sliding window size of 500 kb... 2024/10/29 17:31:01 Finished extracting variants for annotation... 2024/10/29 17:31:01 Start to process figure arts. 2024/10/29 17:31:01 -Processing X ticks... 2024/10/29 17:31:01 -Processing X labels... 2024/10/29 17:31:01 -Processing Y labels... 2024/10/29 17:31:01 -Processing Y tick lables... 2024/10/29 17:31:01 -Processing Y labels... 2024/10/29 17:31:01 -Processing lines... 2024/10/29 17:31:01 Finished processing figure arts. 2024/10/29 17:31:01 Start to annotate variants... 2024/10/29 17:31:01 -Annotating using column CHR:POS... 2024/10/29 17:31:01 -Adjusting text positions with repel_force=0.03... 2024/10/29 17:31:01 Finished annotating variants. 2024/10/29 17:31:01 Start to save figure... 2024/10/29 17:31:01 -Skip saving figure! 2024/10/29 17:31:01 Finished saving figure... 2024/10/29 17:31:01 Finished creating plot successfully! 2024/10/29 17:31:02 Start to create MQQ plot...v3.5.0: 2024/10/29 17:31:02 -Genomic coordinates version: 19... 2024/10/29 17:31:02 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:31:02 -Raw input contains 12557761 variants... 2024/10/29 17:31:02 -MQQ plot layout mode is : m 2024/10/29 17:31:03 Finished loading specified columns from the sumstats. 2024/10/29 17:31:03 Start data conversion and sanity check: 2024/10/29 17:31:03 -Sanity check will be skipped. 2024/10/29 17:31:03 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:31:04 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:31:04 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:31:05 -Converting data above cut line... 2024/10/29 17:31:05 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:31:05 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:31:05 Finished data conversion and sanity check. 2024/10/29 17:31:05 Start to create MQQ plot with 91234 variants... 2024/10/29 17:31:05 -Creating background plot... 2024/10/29 17:31:05 Finished creating MQQ plot successfully! 2024/10/29 17:31:05 Start to extract variants for annotation... 2024/10/29 17:31:05 -Found 16 significant variants with a sliding window size of 500 kb... 2024/10/29 17:31:05 Finished extracting variants for annotation... 2024/10/29 17:31:05 Start to process figure arts. 2024/10/29 17:31:05 -Processing X ticks... 2024/10/29 17:31:05 -Processing X labels... 2024/10/29 17:31:05 -Processing Y labels... 2024/10/29 17:31:05 -Processing Y tick lables... 2024/10/29 17:31:05 -Processing Y labels... 2024/10/29 17:31:05 -Processing lines... 2024/10/29 17:31:05 Finished processing figure arts. 2024/10/29 17:31:05 Start to annotate variants... 2024/10/29 17:31:05 -Annotating using column CHR:POS... 2024/10/29 17:31:05 -Adjusting text positions with repel_force=0.03... 2024/10/29 17:31:05 -Auto-adjusting text positions... 2024/10/29 17:31:10 Finished annotating variants. 2024/10/29 17:31:10 Start to save figure... 2024/10/29 17:31:10 -Skip saving figure! 2024/10/29 17:31:10 Finished saving figure... 2024/10/29 17:31:10 Finished creating plot successfully! 2024/10/29 17:31:14 Start to create MQQ plot...v3.5.0: 2024/10/29 17:31:14 -Genomic coordinates version: 19... 2024/10/29 17:31:14 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:31:14 -Raw input contains 12557761 variants... 2024/10/29 17:31:14 -MQQ plot layout mode is : m 2024/10/29 17:31:14 -Variants to annotate : 1:154309595_TA_T,2:27734972_G_A 2024/10/29 17:31:14 Finished loading specified columns from the sumstats. 2024/10/29 17:31:14 Start data conversion and sanity check: 2024/10/29 17:31:14 -Sanity check will be skipped. 2024/10/29 17:31:15 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:31:15 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:31:16 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:31:17 -Converting data above cut line... 2024/10/29 17:31:17 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:31:17 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:31:17 Finished data conversion and sanity check. 2024/10/29 17:31:17 Start to create MQQ plot with 91234 variants... 2024/10/29 17:31:17 -Creating background plot... 2024/10/29 17:31:17 Finished creating MQQ plot successfully! 2024/10/29 17:31:17 Start to extract variants for annotation... 2024/10/29 17:31:17 -Found 2 specified variants to annotate... 2024/10/29 17:31:17 Start to annotate variants with nearest gene name(s)... 2024/10/29 17:31:17 -Assigning Gene name using ensembl_hg19_gtf for protein coding genes 2024/10/29 17:31:17 Finished annotating variants with nearest gene name(s) successfully! 2024/10/29 17:31:17 Finished extracting variants for annotation... 2024/10/29 17:31:17 Start to process figure arts. 2024/10/29 17:31:17 -Processing X ticks... 2024/10/29 17:31:17 -Processing X labels... 2024/10/29 17:31:17 -Processing Y labels... 2024/10/29 17:31:17 -Processing Y tick lables... 2024/10/29 17:31:17 -Processing Y labels... 2024/10/29 17:31:17 -Processing lines... 2024/10/29 17:31:17 Finished processing figure arts. 2024/10/29 17:31:17 Start to annotate variants... 2024/10/29 17:31:17 -Annotating using column GENENAME... 2024/10/29 17:31:17 -Adjusting text positions with repel_force=0.03... 2024/10/29 17:31:17 Finished annotating variants. 2024/10/29 17:31:17 Start to save figure... 2024/10/29 17:31:17 -Skip saving figure! 2024/10/29 17:31:17 Finished saving figure... 2024/10/29 17:31:17 Finished creating plot successfully! 2024/10/29 17:31:18 Start to create MQQ plot...v3.5.0: 2024/10/29 17:31:18 -Genomic coordinates version: 19... 2024/10/29 17:31:18 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:31:18 -Raw input contains 12557761 variants... 2024/10/29 17:31:18 -MQQ plot layout mode is : m 2024/10/29 17:31:18 -Variants to annotate : 1:154309595_TA_T,2:27734972_G_A 2024/10/29 17:31:19 Finished loading specified columns from the sumstats. 2024/10/29 17:31:19 Start data conversion and sanity check: 2024/10/29 17:31:19 -Removed 0 variants with nan in CHR or POS column ... 2024/10/29 17:31:21 -Removed 0 variants with CHR <=0... 2024/10/29 17:31:21 -Removed 0 variants with nan in P column ... 2024/10/29 17:31:22 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:31:22 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:31:22 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:31:23 -Converting data above cut line... 2024/10/29 17:31:23 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:31:23 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:31:23 Finished data conversion and sanity check. 2024/10/29 17:31:23 Start to create MQQ plot with 91234 variants... 2024/10/29 17:31:23 -Creating background plot... 2024/10/29 17:31:24 Finished creating MQQ plot successfully! 2024/10/29 17:31:24 Start to extract variants for annotation... 2024/10/29 17:31:24 -Found 2 specified variants to annotate... 2024/10/29 17:31:24 Finished extracting variants for annotation... 2024/10/29 17:31:24 Start to process figure arts. 2024/10/29 17:31:24 -Processing X ticks... 2024/10/29 17:31:24 -Processing X labels... 2024/10/29 17:31:24 -Processing Y labels... 2024/10/29 17:31:24 -Processing Y tick lables... 2024/10/29 17:31:24 -Processing Y labels... 2024/10/29 17:31:24 -Processing lines... 2024/10/29 17:31:24 Finished processing figure arts. 2024/10/29 17:31:24 Start to annotate variants... 2024/10/29 17:31:24 -Annotating using column CHR:POS... 2024/10/29 17:31:24 -Adjusting text positions with repel_force=0.03... 2024/10/29 17:31:24 Finished annotating variants. 2024/10/29 17:31:24 Start to save figure... 2024/10/29 17:31:24 -Skip saving figure! 2024/10/29 17:31:24 Finished saving figure... 2024/10/29 17:31:24 Finished creating plot successfully! 2024/10/29 17:31:24 Start to create MQQ plot...v3.5.0: 2024/10/29 17:31:24 -Genomic coordinates version: 19... 2024/10/29 17:31:24 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:31:24 -Raw input contains 12557761 variants... 2024/10/29 17:31:24 -MQQ plot layout mode is : m 2024/10/29 17:31:24 -Variants to annotate : 2:27734972_G_A,2:27734972_G_A,7:127253550_C_T,19:46166604_C_T 2024/10/29 17:31:24 -Loci to highlight (#CB132D): 19:46166604_C_T,1:154309595_TA_T,7:127253550_C_T 2024/10/29 17:31:24 -highlight_windowkb is set to: 1000 kb 2024/10/29 17:31:24 -Variants to pinpoint (red) : 2:27734972_G_A 2024/10/29 17:31:26 Finished loading specified columns from the sumstats. 2024/10/29 17:31:26 Start data conversion and sanity check: 2024/10/29 17:31:26 -Sanity check will be skipped. 2024/10/29 17:31:27 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:31:27 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:31:28 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:31:29 -Converting data above cut line... 2024/10/29 17:31:29 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:31:29 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:31:29 Finished data conversion and sanity check. 2024/10/29 17:31:29 Start to create MQQ plot with 91234 variants... 2024/10/29 17:31:29 -Creating background plot... 2024/10/29 17:31:29 -Highlighting target loci... 2024/10/29 17:31:29 -Pinpointing target vairants... 2024/10/29 17:31:29 Finished creating MQQ plot successfully! 2024/10/29 17:31:29 Start to extract variants for annotation... 2024/10/29 17:31:29 -Found 3 specified variants to annotate... 2024/10/29 17:31:29 Finished extracting variants for annotation... 2024/10/29 17:31:29 Start to process figure arts. 2024/10/29 17:31:29 -Processing X ticks... 2024/10/29 17:31:29 -Processing X labels... 2024/10/29 17:31:29 -Processing Y labels... 2024/10/29 17:31:29 -Processing Y tick lables... 2024/10/29 17:31:29 -Processing Y labels... 2024/10/29 17:31:29 -Processing lines... 2024/10/29 17:31:29 Finished processing figure arts. 2024/10/29 17:31:29 Start to annotate variants... 2024/10/29 17:31:29 -Annotating using column CHR:POS... 2024/10/29 17:31:29 -Adjusting text positions with repel_force=0.03... 2024/10/29 17:31:29 Finished annotating variants. 2024/10/29 17:31:29 Start to save figure... 2024/10/29 17:31:29 -Skip saving figure! 2024/10/29 17:31:29 Finished saving figure... 2024/10/29 17:31:29 Finished creating plot successfully! 2024/10/29 17:31:30 Start to create MQQ plot...v3.5.0: 2024/10/29 17:31:30 -Genomic coordinates version: 19... 2024/10/29 17:31:30 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:31:30 -Raw input contains 12557761 variants... 2024/10/29 17:31:30 -MQQ plot layout mode is : m 2024/10/29 17:31:30 -Set 1 loci to highlight (yellow) : 19:46166604_C_T,1:154309595_TA_T 2024/10/29 17:31:30 -Set 2 loci to highlight (red) : X:57170781_A_AT,7:127253550_C_T 2024/10/29 17:31:30 -highlight_windowkb is set to: 1000 kb 2024/10/29 17:31:31 Finished loading specified columns from the sumstats. 2024/10/29 17:31:31 Start data conversion and sanity check: 2024/10/29 17:31:31 -Sanity check will be skipped. 2024/10/29 17:31:33 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:31:33 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:31:34 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:31:35 -Converting data above cut line... 2024/10/29 17:31:35 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:31:35 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:31:35 Finished data conversion and sanity check. 2024/10/29 17:31:35 Start to create MQQ plot with 91234 variants... 2024/10/29 17:31:35 -Creating background plot... 2024/10/29 17:31:35 -Highlighting set 1 target loci... 2024/10/29 17:31:35 -Highlighting set 2 target loci... 2024/10/29 17:31:35 Finished creating MQQ plot successfully! 2024/10/29 17:31:35 Start to extract variants for annotation... 2024/10/29 17:31:35 -Found 89 significant variants with a sliding window size of 500 kb... 2024/10/29 17:31:35 Finished extracting variants for annotation... 2024/10/29 17:31:35 Start to process figure arts. 2024/10/29 17:31:35 -Processing X ticks... 2024/10/29 17:31:35 -Processing X labels... 2024/10/29 17:31:35 -Processing Y labels... 2024/10/29 17:31:35 -Processing Y tick lables... 2024/10/29 17:31:35 -Processing Y labels... 2024/10/29 17:31:35 -Processing lines... 2024/10/29 17:31:35 Finished processing figure arts. 2024/10/29 17:31:35 Start to annotate variants... 2024/10/29 17:31:35 -Skip annotating 2024/10/29 17:31:35 Finished annotating variants. 2024/10/29 17:31:35 Start to save figure... 2024/10/29 17:31:35 -Skip saving figure! 2024/10/29 17:31:35 Finished saving figure... 2024/10/29 17:31:35 Finished creating plot successfully! 2024/10/29 17:31:36 Start to create MQQ plot...v3.5.0: 2024/10/29 17:31:36 -Genomic coordinates version: 19... 2024/10/29 17:31:36 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:31:36 -Raw input contains 12557761 variants... 2024/10/29 17:31:36 -MQQ plot layout mode is : mqq 2024/10/29 17:31:38 Finished loading specified columns from the sumstats. 2024/10/29 17:31:38 Start data conversion and sanity check: 2024/10/29 17:31:38 -Sanity check will be skipped. 2024/10/29 17:31:38 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:31:39 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:31:39 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:31:40 -Converting data above cut line... 2024/10/29 17:31:40 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:31:40 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:31:40 Finished data conversion and sanity check. 2024/10/29 17:31:40 Start to create MQQ plot with 91234 variants... 2024/10/29 17:31:40 -Creating background plot... 2024/10/29 17:31:40 Finished creating MQQ plot successfully! 2024/10/29 17:31:40 Start to extract variants for annotation... 2024/10/29 17:31:41 -Found 89 significant variants with a sliding window size of 500 kb... 2024/10/29 17:31:41 Finished extracting variants for annotation... 2024/10/29 17:31:41 Start to process figure arts. 2024/10/29 17:31:41 -Processing X ticks... 2024/10/29 17:31:41 -Processing X labels... 2024/10/29 17:31:41 -Processing Y labels... 2024/10/29 17:31:41 -Processing Y tick lables... 2024/10/29 17:31:41 -Processing Y labels... 2024/10/29 17:31:41 -Processing lines... 2024/10/29 17:31:41 Finished processing figure arts. 2024/10/29 17:31:41 Start to annotate variants... 2024/10/29 17:31:41 -Skip annotating 2024/10/29 17:31:41 Finished annotating variants. 2024/10/29 17:31:41 Start to create QQ plot with 91234 variants: 2024/10/29 17:31:41 -Plotting variants stratified by MAF... 2024/10/29 17:31:42 -Lambda GC (MLOG10P mode) at 0.5 is 1.21283 2024/10/29 17:31:42 -Processing Y tick lables... 2024/10/29 17:31:42 Finished creating QQ plot successfully! 2024/10/29 17:31:42 Start to save figure... 2024/10/29 17:31:42 -Skip saving figure! 2024/10/29 17:31:42 Finished saving figure... 2024/10/29 17:31:42 Finished creating plot successfully! 2024/10/29 17:31:43 Start to create MQQ plot...v3.5.0: 2024/10/29 17:31:43 -Genomic coordinates version: 19... 2024/10/29 17:31:43 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:31:43 -Raw input contains 12557761 variants... 2024/10/29 17:31:43 -MQQ plot layout mode is : m 2024/10/29 17:31:44 Finished loading specified columns from the sumstats. 2024/10/29 17:31:44 Start data conversion and sanity check: 2024/10/29 17:31:44 -Sanity check will be skipped. 2024/10/29 17:31:45 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:31:45 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:31:46 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:31:47 -Converting data above cut line... 2024/10/29 17:31:47 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:31:47 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:31:47 Finished data conversion and sanity check. 2024/10/29 17:31:47 Start to create MQQ plot with 91234 variants... 2024/10/29 17:31:47 -Creating background plot... 2024/10/29 17:31:47 Finished creating MQQ plot successfully! 2024/10/29 17:31:47 Start to extract variants for annotation... 2024/10/29 17:31:47 -Found 20 significant variants with a sliding window size of 1000000 kb... 2024/10/29 17:31:47 Start to annotate variants with nearest gene name(s)... 2024/10/29 17:31:47 -Assigning Gene name using ensembl_hg19_gtf for protein coding genes 2024/10/29 17:31:48 Finished annotating variants with nearest gene name(s) successfully! 2024/10/29 17:31:48 Finished extracting variants for annotation... 2024/10/29 17:31:48 Start to process figure arts. 2024/10/29 17:31:48 -Processing X ticks... 2024/10/29 17:31:48 -Processing X labels... 2024/10/29 17:31:48 -Processing Y labels... 2024/10/29 17:31:48 -Processing Y tick lables... 2024/10/29 17:31:48 -Processing Y labels... 2024/10/29 17:31:48 -Processing lines... 2024/10/29 17:31:48 Finished processing figure arts. 2024/10/29 17:31:48 Start to annotate variants... 2024/10/29 17:31:48 -Annotating using column GENENAME... 2024/10/29 17:31:48 -Adjusting text positions with repel_force=0.03... 2024/10/29 17:31:48 Finished annotating variants. 2024/10/29 17:31:48 Start to save figure... 2024/10/29 17:31:48 -Skip saving figure! 2024/10/29 17:31:48 Finished saving figure... 2024/10/29 17:31:48 Finished creating plot successfully! 2024/10/29 17:31:49 Start to create MQQ plot...v3.5.0: 2024/10/29 17:31:49 -Genomic coordinates version: 19... 2024/10/29 17:31:49 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:31:49 -Raw input contains 12557761 variants... 2024/10/29 17:31:49 -MQQ plot layout mode is : m 2024/10/29 17:31:50 Finished loading specified columns from the sumstats. 2024/10/29 17:31:50 Start data conversion and sanity check: 2024/10/29 17:31:50 -Sanity check will be skipped. 2024/10/29 17:31:50 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:31:51 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:31:51 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:31:52 -Converting data above cut line... 2024/10/29 17:31:52 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:31:52 Finished data conversion and sanity check. 2024/10/29 17:31:52 Start to create MQQ plot with 91234 variants... 2024/10/29 17:31:52 -Creating background plot... 2024/10/29 17:31:52 Finished creating MQQ plot successfully! 2024/10/29 17:31:52 Start to extract variants for annotation... 2024/10/29 17:31:53 -Found 20 significant variants with a sliding window size of 1000000 kb... 2024/10/29 17:31:53 Start to annotate variants with nearest gene name(s)... 2024/10/29 17:31:53 -Assigning Gene name using ensembl_hg19_gtf for protein coding genes 2024/10/29 17:31:53 Finished annotating variants with nearest gene name(s) successfully! 2024/10/29 17:31:53 Finished extracting variants for annotation... 2024/10/29 17:31:53 Start to process figure arts. 2024/10/29 17:31:53 -Processing X ticks... 2024/10/29 17:31:53 -Processing X labels... 2024/10/29 17:31:53 -Processing Y labels... 2024/10/29 17:31:53 -Processing Y tick lables... 2024/10/29 17:31:53 -Processing Y labels... 2024/10/29 17:31:53 -Processing lines... 2024/10/29 17:31:53 Finished processing figure arts. 2024/10/29 17:31:53 Start to annotate variants... 2024/10/29 17:31:53 -Annotating using column GENENAME... 2024/10/29 17:31:53 -Adjusting text positions with repel_force=0.03... 2024/10/29 17:31:53 Finished annotating variants. 2024/10/29 17:31:53 Start to save figure... 2024/10/29 17:31:53 -Skip saving figure! 2024/10/29 17:31:53 Finished saving figure... 2024/10/29 17:31:53 Finished creating plot successfully! 2024/10/29 17:31:54 Start to create MQQ plot...v3.5.0: 2024/10/29 17:31:54 -Genomic coordinates version: 19... 2024/10/29 17:31:54 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:31:54 -Raw input contains 12557761 variants... 2024/10/29 17:31:54 -MQQ plot layout mode is : mqq 2024/10/29 17:31:54 -Loci to highlight (purple): 7:127253550_C_T 2024/10/29 17:31:54 -highlight_windowkb is set to: 500 kb 2024/10/29 17:31:54 -Variants to pinpoint (green) : 2:27734972_G_A 2024/10/29 17:31:56 Finished loading specified columns from the sumstats. 2024/10/29 17:31:56 Start data conversion and sanity check: 2024/10/29 17:31:56 -Sanity check will be skipped. 2024/10/29 17:31:57 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:31:58 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:31:58 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:31:59 -Converting data above cut line... 2024/10/29 17:31:59 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:31:59 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:31:59 Finished data conversion and sanity check. 2024/10/29 17:31:59 Start to create MQQ plot with 91234 variants... 2024/10/29 17:31:59 -Creating background plot... 2024/10/29 17:32:00 -Highlighting target loci... 2024/10/29 17:32:00 -Pinpointing target vairants... 2024/10/29 17:32:00 Finished creating MQQ plot successfully! 2024/10/29 17:32:00 Start to extract variants for annotation... 2024/10/29 17:32:00 -Found 89 significant variants with a sliding window size of 500 kb... 2024/10/29 17:32:00 Finished extracting variants for annotation... 2024/10/29 17:32:00 Start to process figure arts. 2024/10/29 17:32:00 -Processing X ticks... 2024/10/29 17:32:00 -Processing X labels... 2024/10/29 17:32:00 -Processing Y labels... 2024/10/29 17:32:00 -Processing Y tick lables... 2024/10/29 17:32:00 -Processing Y labels... 2024/10/29 17:32:00 -Processing lines... 2024/10/29 17:32:00 Finished processing figure arts. 2024/10/29 17:32:00 Start to annotate variants... 2024/10/29 17:32:00 -Skip annotating 2024/10/29 17:32:00 Finished annotating variants. 2024/10/29 17:32:00 Start to create QQ plot with 91234 variants: 2024/10/29 17:32:00 -Plotting variants stratified by MAF... 2024/10/29 17:32:01 -Lambda GC (MLOG10P mode) at 0.5 is 1.21283 2024/10/29 17:32:01 -Processing Y tick lables... 2024/10/29 17:32:01 Finished creating QQ plot successfully! 2024/10/29 17:32:01 Start to save figure... 2024/10/29 17:32:01 -Skip saving figure! 2024/10/29 17:32:01 Finished saving figure... 2024/10/29 17:32:01 Finished creating plot successfully! 2024/10/29 17:32:02 Start to create MQQ plot...v3.5.0: 2024/10/29 17:32:02 -Genomic coordinates version: 19... 2024/10/29 17:32:02 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:32:02 -Raw input contains 12557761 variants... 2024/10/29 17:32:02 -MQQ plot layout mode is : mqq 2024/10/29 17:32:04 Finished loading specified columns from the sumstats. 2024/10/29 17:32:04 Start data conversion and sanity check: 2024/10/29 17:32:04 -Removed 0 variants with nan in CHR or POS column ... 2024/10/29 17:32:06 -Removed 0 variants with CHR <=0... 2024/10/29 17:32:07 -Removed 0 variants with nan in EAF column ... 2024/10/29 17:32:07 -Removed 0 variants with nan in P column ... 2024/10/29 17:32:07 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:32:08 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:32:08 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:32:09 -Converting data above cut line... 2024/10/29 17:32:09 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:32:09 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:32:09 Finished data conversion and sanity check. 2024/10/29 17:32:09 Start to create MQQ plot with 91234 variants... 2024/10/29 17:32:09 -Creating background plot... 2024/10/29 17:32:09 Finished creating MQQ plot successfully! 2024/10/29 17:32:09 Start to extract variants for annotation... 2024/10/29 17:32:10 -Found 89 significant variants with a sliding window size of 500 kb... 2024/10/29 17:32:10 Finished extracting variants for annotation... 2024/10/29 17:32:10 Start to process figure arts. 2024/10/29 17:32:10 -Processing X ticks... 2024/10/29 17:32:10 -Processing X labels... 2024/10/29 17:32:10 -Processing Y labels... 2024/10/29 17:32:10 -Processing Y tick lables... 2024/10/29 17:32:10 -Processing Y labels... 2024/10/29 17:32:10 -Processing lines... 2024/10/29 17:32:10 Finished processing figure arts. 2024/10/29 17:32:10 Start to annotate variants... 2024/10/29 17:32:10 -Skip annotating 2024/10/29 17:32:10 Finished annotating variants. 2024/10/29 17:32:10 Start to create QQ plot with 91234 variants: 2024/10/29 17:32:10 -Plotting variants stratified by MAF... 2024/10/29 17:32:11 -Lambda GC (MLOG10P mode) at 0.5 is 1.21283 2024/10/29 17:32:11 -Processing Y tick lables... 2024/10/29 17:32:11 Finished creating QQ plot successfully! 2024/10/29 17:32:11 Start to save figure... 2024/10/29 17:32:12 -Saved to my_maf_stratified_mqq_plot.png successfully! (overwrite) 2024/10/29 17:32:12 Finished saving figure... 2024/10/29 17:32:12 Finished creating plot successfully! 2024/10/29 17:32:14 Start to create MQQ plot...v3.5.0: 2024/10/29 17:32:14 -Genomic coordinates version: 19... 2024/10/29 17:32:14 -Genome-wide significance level to plot is set to 5e-08 ... 2024/10/29 17:32:14 -Raw input contains 12557761 variants... 2024/10/29 17:32:14 -MQQ plot layout mode is : mqq 2024/10/29 17:32:15 Finished loading specified columns from the sumstats. 2024/10/29 17:32:15 Start data conversion and sanity check: 2024/10/29 17:32:16 -Removed 0 variants with nan in CHR or POS column ... 2024/10/29 17:32:17 -Removed 0 variants with CHR <=0... 2024/10/29 17:32:18 -Removed 0 variants with nan in EAF column ... 2024/10/29 17:32:18 -Removed 0 variants with nan in P column ... 2024/10/29 17:32:18 -Sanity check after conversion: 0 variants with P value outside of (0,1] will be removed... 2024/10/29 17:32:19 -Sumstats P values are being converted to -log10(P)... 2024/10/29 17:32:19 -Sanity check: 0 na/inf/-inf variants will be removed... 2024/10/29 17:32:20 -Converting data above cut line... 2024/10/29 17:32:20 -Maximum -log10(P) value is 167.58838029403677 . 2024/10/29 17:32:20 -Minus log10(P) values above 20 will be shrunk with a shrinkage factor of 10... 2024/10/29 17:32:20 Finished data conversion and sanity check. 2024/10/29 17:32:20 Start to create MQQ plot with 91234 variants... 2024/10/29 17:32:20 -Creating background plot... 2024/10/29 17:32:21 Finished creating MQQ plot successfully! 2024/10/29 17:32:21 Start to extract variants for annotation... 2024/10/29 17:32:21 -Found 89 significant variants with a sliding window size of 500 kb... 2024/10/29 17:32:21 Finished extracting variants for annotation... 2024/10/29 17:32:21 Start to process figure arts. 2024/10/29 17:32:21 -Processing X ticks... 2024/10/29 17:32:21 -Processing X labels... 2024/10/29 17:32:21 -Processing Y labels... 2024/10/29 17:32:21 -Processing Y tick lables... 2024/10/29 17:32:21 -Processing Y labels... 2024/10/29 17:32:21 -Processing lines... 2024/10/29 17:32:21 Finished processing figure arts. 2024/10/29 17:32:21 Start to annotate variants... 2024/10/29 17:32:21 -Skip annotating 2024/10/29 17:32:21 Finished annotating variants. 2024/10/29 17:32:21 Start to create QQ plot with 91234 variants: 2024/10/29 17:32:21 -Plotting variants stratified by MAF... 2024/10/29 17:32:22 -Lambda GC (MLOG10P mode) at 0.5 is 1.21283 2024/10/29 17:32:22 -Processing Y tick lables... 2024/10/29 17:32:22 Finished creating QQ plot successfully! 2024/10/29 17:32:22 Start to save figure... 2024/10/29 17:32:22 -Skip saving figure! 2024/10/29 17:32:22 Finished saving figure... 2024/10/29 17:32:22 Finished creating plot successfully!