Stacked Manhattan and regional plot

Load gwaslab and sumstats

Example

import gwaslab as gl

Example

gl.show_version()

stdout:

2025/12/25 23:54:24 GWASLab v4.0.0 https://cloufield.github.io/gwaslab/
2025/12/25 23:54:24 (C) 2022-2025, Yunye He, Kamatani Lab, GPL-3.0 license, gwaslab@gmail.com
2025/12/25 23:54:24 Python version: 3.12.0 | packaged by conda-forge | (main, Oct  3 2023, 08:43:22) [GCC 12.3.0]

Example

gl1 = gl.Sumstats("../0_sample_data/bbj_bmi_female.txt.gz",beta="BETA",se="SE",snpid="SNP",chrom="CHR",ea="ALT",nea="REF",pos="POS",p="P", build="19",sep="\t", verbose=False)
gl2 = gl.Sumstats("../0_sample_data/bbj_bmi_male.txt.gz",snpid="SNP",chrom="CHR",ea="ALT",nea="REF",pos="POS",p="P", build="19",sep="\t", verbose=False)

gl1.basic_check(verbose=False)
gl2.basic_check(verbose=False)

SNPID	CHR	POS	EA	NEA	STATUS	P
rs143225517	1	751756	C	T	1980099	0.5883
rs3094315	1	752566	A	G	1980099	0.5889
rs61770173	1	753405	A	C	1980099	0.5878
rs117086422	1	845635	T	C	1980099	0.5565
rs28612348	1	846078	T	C	1980099	0.5659
...	...	...	...	...	...	...
rs41281537	22	51171667	A	G	1980099	0.8453
rs756638	22	51171693	A	G	1980099	0.7726
rs5770824	22	51172460	C	T	1980099	0.8374
rs3810648	22	51175626	G	A	1980099	0.2884
rs2285395	22	51178090	A	G	1980099	0.3223

Example

gl.plot_stacked_mqq(objects=[gl1,gl2],
                    vcfs=[gl.get_path("1kg_eas_hg19"), gl.get_path("1kg_eas_hg19")],
                    region_legend_marker=False,
                    region=(19,46214297 - 100000, 46214297 + 100000),
                    region_ref =["rs35560038","rs1055220","rs4802274"],
                    build="19",
                    anno="SNPID",
                    fontsize=15,
                    mode="r",
                    region_chromatin_files=["../0_sample_data/E098_15_coreMarks_mnemonics.bed.gz"],
                    region_chromatin_labels=["E098_15"],
                    cbar_fontsize=11,
                    marker_size=(100,100),
                    titles=["Male","Female"],
                    title_kwargs={"size":20},
                    anno_kwargs={"rotation":0,"fontsize":10}, 
                    verbose=False, check=False)

stdout:

2025/12/25 23:55:37  -POS data type is already numeric. Skipping conversion...
2025/12/25 23:55:37  -CHR data type is already numeric. Skipping conversion...
2025/12/25 23:55:47  -POS data type is already numeric. Skipping conversion...
2025/12/25 23:55:47  -CHR data type is already numeric. Skipping conversion...

(<Figure size 3200x3200 with 7 Axes>,
 <gwaslab.info.g_Log.Log at 0x7fd21de3fb30>)

Output image

Stacked Manhattan plot

Example

gl.plot_stacked_mqq(objects=[gl1,gl2],
                    mode="m",
                    skip=3,
                    titles=["Female - BMI","Male - BMI"],
                    check=False,
                    verbose=False)

stdout:

2025/12/25 23:55:52 #WARNING! Genomic coordinates version is unknown.
2025/12/25 23:55:54  -POS data type is already numeric. Skipping conversion...
2025/12/25 23:55:54  -CHR data type is already numeric. Skipping conversion...
2025/12/25 23:55:57 #WARNING! Genomic coordinates version is unknown.
2025/12/25 23:55:59  -POS data type is already numeric. Skipping conversion...
2025/12/25 23:55:59  -CHR data type is already numeric. Skipping conversion...

(<Figure size 2000x1600 with 2 Axes>,
 <gwaslab.info.g_Log.Log at 0x7fd21de3fb30>)

Output image

Multiple stacked plots

Example

#gl.download_ref("1kg_eas_hg19")

Example

gl.plot_stacked_mqq(objects=[gl1,gl1,gl1,gl1],
                    mode="m",
                    skip=3,
                    titles=["BMI 1","BMI 2", "BMI 3", "BMI 4"],
                    check=False,
                    verbose=False)

stdout:

2025/12/25 23:56:03 #WARNING! Genomic coordinates version is unknown.
2025/12/25 23:56:05  -POS data type is already numeric. Skipping conversion...
2025/12/25 23:56:05  -CHR data type is already numeric. Skipping conversion...
2025/12/25 23:56:07 #WARNING! Genomic coordinates version is unknown.
2025/12/25 23:56:09  -POS data type is already numeric. Skipping conversion...
2025/12/25 23:56:09  -CHR data type is already numeric. Skipping conversion...
2025/12/25 23:56:12 #WARNING! Genomic coordinates version is unknown.
2025/12/25 23:56:14  -POS data type is already numeric. Skipping conversion...
2025/12/25 23:56:14  -CHR data type is already numeric. Skipping conversion...
2025/12/25 23:56:16 #WARNING! Genomic coordinates version is unknown.
2025/12/25 23:56:18  -POS data type is already numeric. Skipping conversion...
2025/12/25 23:56:18  -CHR data type is already numeric. Skipping conversion...

(<Figure size 2000x3200 with 4 Axes>,
 <gwaslab.info.g_Log.Log at 0x7fd21de3fb30>)

Output image

Add title and annotation

Example

gl.plot_stacked_mqq(objects=[gl1,gl2],
                    mode="m",
                    skip=3,
                    anno=True,
                    anno_style="right",
                    titles=["Female - BMI","Male - BMI"],
                    region_hspace=0.4,   # increase the space between each subplot
                    xpadl=0.05,          # increase left padding for X axis
                    title_pos=[0, 1.7],  # adjust title position
                    check=False,
                    verbose=False)

stdout:

2025/12/25 23:56:22 #WARNING! Genomic coordinates version is unknown.
2025/12/25 23:56:24  -POS data type is already numeric. Skipping conversion...
2025/12/25 23:56:24  -CHR data type is already numeric. Skipping conversion...
2025/12/25 23:56:27 #WARNING! Genomic coordinates version is unknown.
2025/12/25 23:56:28  -POS data type is already numeric. Skipping conversion...
2025/12/25 23:56:28  -CHR data type is already numeric. Skipping conversion...

(<Figure size 2000x1600 with 2 Axes>,
 <gwaslab.info.g_Log.Log at 0x7fd21de3fb30>)

Output image

Customization

You can customize each plot using options for plot_mqq() by adding a number to the end of the option like highlight1 means highlight option for the first panel. if no number suffix was added, the option will be applied to all panels.

Example

gl.plot_stacked_mqq(objects=[gl1,gl2],
                    mode="m",
                    skip=3,
                    anno=True,
                    anno_style="expand",
                    titles=["Female - BMI","Male - BMI"],
                    highlight1=["rs183975233"],
                    highlight2=["rs35560038"],
                    anno_set1=["rs183975233"],
                    anno_set2=["rs35560038"],
                    region_hspace=0.4,   # increase the space between each subplot
                    xpadl=0.05,          # increase left padding for X axis
                    title_pos=[0, 1.3],  # adjust title position
                    check=False,
                    verbose=False)

stdout:

2025/12/25 23:56:33 #WARNING! Genomic coordinates version is unknown.
2025/12/25 23:56:35  -POS data type is already numeric. Skipping conversion...
2025/12/25 23:56:35  -CHR data type is already numeric. Skipping conversion...
2025/12/25 23:56:40 #WARNING! Genomic coordinates version is unknown.
2025/12/25 23:56:41  -POS data type is already numeric. Skipping conversion...
2025/12/25 23:56:41  -CHR data type is already numeric. Skipping conversion...

(<Figure size 2000x1600 with 2 Axes>,
 <gwaslab.info.g_Log.Log at 0x7fd21de3fb30>)

Output image

Stacked regional plot

Example

gl2.filter_flanking_by_chrpos((19,46214297)).filter_value("P <1e-20").data

stdout:

2025/12/25 23:56:48 Start to extract variants in the flanking regions using CHR and POS ...(v4.0.0)
2025/12/25 23:56:48  -Current Dataframe shape : 5961600 x 7 ; Memory usage: 255.84 MB
2025/12/25 23:56:48  - Central positions: (19, 46214297)
2025/12/25 23:56:48  - Flanking windowsize in kb: 500
2025/12/25 23:56:48  - Variants in flanking region 19:45714297-46714297 : 2137
2025/12/25 23:56:48  - Extracted 2137 variants in the regions.
2025/12/25 23:56:48  -Filtered out variants: 5959463
2025/12/25 23:56:48  -Current Dataframe shape : 2137 x 7 ; Memory usage: 0.11 MB
2025/12/25 23:56:48 Finished extracting variants in the flanking regions.
2025/12/25 23:56:48 Start to filter variants by condition... ...(v4.0.0)
2025/12/25 23:56:48  -Current Dataframe shape : 2137 x 7 ; Memory usage: 0.11 MB
2025/12/25 23:56:48  -Expression: P <1e-20
2025/12/25 23:56:49  -Filtered out variants: 2131
2025/12/25 23:56:49  -Current Dataframe shape : 6 x 7 ; Memory usage: 0.00 MB
2025/12/25 23:56:49 Finished filtering variants.

SNPID	CHR	POS	EA	NEA	STATUS	P
rs35560038	19	46175046	T	A	1980099	1.643000e-24
rs34089191	19	46176723	C	G	1980099	5.961000e-21
rs55669001	19	46177235	C	T	1980099	9.950000e-21
rs9676912	19	46212182	T	C	1980099	5.247000e-22
rs8101428	19	46212952	C	T	1980099	1.094000e-22
rs1055220	19	46214297	T	C	1980099	5.731000e-24

stacked regional plots with single reference SNP

Example

gl.plot_stacked_mqq(objects=[gl1,gl2],
                    vcfs=[gl.get_path("1kg_eas_hg19"), gl.get_path("1kg_eas_hg19")],
                    region=(19,46214297 - 300000, 46214297 + 300000),
                    build="19",
                    mode="r",
                    anno="SNPID",
                    anno_style="tight",
                    titles=["Male","Female"],
                    title_kwargs={"size":20},
                    anno_kwargs={"rotation":0}, verbose=False, check=False)

stdout:

2025/12/25 23:56:52  -POS data type is already numeric. Skipping conversion...
2025/12/25 23:56:52  -CHR data type is already numeric. Skipping conversion...
2025/12/25 23:57:05  -POS data type is already numeric. Skipping conversion...
2025/12/25 23:57:05  -CHR data type is already numeric. Skipping conversion...

(<Figure size 3200x2400 with 6 Axes>,
 <gwaslab.info.g_Log.Log at 0x7fd21de3fb30>)

Output image

stacked regional plots with multiple reference SNPs

Example

gl.plot_stacked_mqq(objects=[gl1,gl2],
                    vcfs=[gl.get_path("1kg_eas_hg19"), gl.get_path("1kg_eas_hg19")],
                    region=(19,46214297 - 100000, 46214297 + 100000),
                    region_ref =["rs35560038","rs1055220","rs4802274"],
                    build="19",
                    anno="SNPID",
                    anno_set =["rs35560038","rs1055220","rs4802274"],
                    mode="r",
                    anno_style="tight",anno_adjust=True,
                    cbar_fontsize=11,
                    anno_xshift=0.01,
                    marker_size=(100,100),
                    titles=["Male","Female"],
                    title_kwargs={"size":20},
                    anno_kwargs={"rotation":0,"fontsize":12}, verbose=False, check=False)

stdout:

2025/12/25 23:57:13  -POS data type is already numeric. Skipping conversion...
2025/12/25 23:57:13  -CHR data type is already numeric. Skipping conversion...
2025/12/25 23:57:24  -POS data type is already numeric. Skipping conversion...
2025/12/25 23:57:24  -CHR data type is already numeric. Skipping conversion...

(<Figure size 3200x2400 with 6 Axes>,
 <gwaslab.info.g_Log.Log at 0x7fd21de3fb30>)

Output image

Stacked regional plots with chromatin status

Example

gl.plot_stacked_mqq(objects=[gl1,gl2],
                    vcfs=[gl.get_path("1kg_eas_hg19"), gl.get_path("1kg_eas_hg19")],
                    region=(19,46214297 - 100000, 46214297 + 100000),
                    region_ref =["rs35560038","rs1055220","rs4802274"],
                    build="19",
                    anno="SNPID",
                    fontsize=15,
                    mode="r",
                    region_chromatin_files=["../0_sample_data/E098_15_coreMarks_mnemonics.bed.gz"],
                    region_chromatin_labels=["E098_15"],
                    cbar_fontsize=11,
                    anno_xshift=0.01,
                    marker_size=(100,100),
                    titles=["Male","Female"],
                    title_kwargs={"size":20},
                    anno_kwargs={"rotation":0,"fontsize":10}, 
                    verbose=False, check=False)

stdout:

2025/12/25 23:57:30  -POS data type is already numeric. Skipping conversion...
2025/12/25 23:57:30  -CHR data type is already numeric. Skipping conversion...
2025/12/25 23:57:40  -POS data type is already numeric. Skipping conversion...
2025/12/25 23:57:40  -CHR data type is already numeric. Skipping conversion...

(<Figure size 3200x3200 with 7 Axes>,
 <gwaslab.info.g_Log.Log at 0x7fd21de3fb30>)

Output image

turn off legend marker

Example

gl.plot_stacked_mqq(objects=[gl1,gl2],
                    vcfs=[gl.get_path("1kg_eas_hg19"), gl.get_path("1kg_eas_hg19")],
                    region_legend_marker=False,
                    region=(19,46214297 - 100000, 46214297 + 100000),
                    region_ref =["rs35560038","rs1055220","rs4802274"],
                    build="19",
                    anno="SNPID",
                    fontsize=15,
                    mode="r",
                    region_chromatin_files=["../0_sample_data/E098_15_coreMarks_mnemonics.bed.gz"],
                    region_chromatin_labels=["E098_15"],
                    cbar_fontsize=11,
                    marker_size=(100,100),
                    titles=["Male","Female"],
                    title_kwargs={"size":20},
                    anno_kwargs={"rotation":0,"fontsize":10}, 
                    verbose=False, check=False)

stdout:

2025/12/25 23:57:49  -POS data type is already numeric. Skipping conversion...
2025/12/25 23:57:49  -CHR data type is already numeric. Skipping conversion...
2025/12/25 23:57:59  -POS data type is already numeric. Skipping conversion...
2025/12/25 23:57:59  -CHR data type is already numeric. Skipping conversion...

(<Figure size 3200x3200 with 7 Axes>,
 <gwaslab.info.g_Log.Log at 0x7fd21de3fb30>)

Output image