Stacked Manhattan and regional plot¶

Load gwaslab and sumstats¶

Note: Available since v3.4.39

In [1]:

import gwaslab as gl

import gwaslab as gl

In [2]:

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

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

Stacked Manhattan plot¶

In [3]:

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

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

2024/07/02 14:19:45  #WARNING! Genomic coordinates version is unknown.
2024/07/02 14:19:47  #WARNING! Genomic coordinates version is unknown.

Out[3]:

(<Figure size 2000x1600 with 2 Axes>, <gwaslab.g_Log.Log at 0x7fc603263f10>)

Multiple subplots¶

In [4]:

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)

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)

2024/07/02 14:19:51  #WARNING! Genomic coordinates version is unknown.
2024/07/02 14:19:54  #WARNING! Genomic coordinates version is unknown.
2024/07/02 14:19:57  #WARNING! Genomic coordinates version is unknown.
2024/07/02 14:20:00  #WARNING! Genomic coordinates version is unknown.

Out[4]:

(<Figure size 2000x3200 with 4 Axes>, <gwaslab.g_Log.Log at 0x7fc603263f10>)

Add title and annotation¶

In [5]:

gl.plot_stacked_mqq(objects=[gl1,gl2],
                    mode="m",
                    skip=3,
                    anno=True,
                    anno_style="expand",
                    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, 1.3],  # adjust title position
                    check=False,
                    verbose=False)

gl.plot_stacked_mqq(objects=[gl1,gl2], mode="m", skip=3, anno=True, anno_style="expand", 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, 1.3], # adjust title position check=False, verbose=False)

2024/07/02 14:20:04  #WARNING! Genomic coordinates version is unknown.
2024/07/02 14:20:06  #WARNING! Genomic coordinates version is unknown.

Out[5]:

(<Figure size 2000x1600 with 2 Axes>, <gwaslab.g_Log.Log at 0x7fc603263f10>)

Stacked regional plot¶

In [6]:

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=True,
                    anno_style="tight",
                    titles=["Male","Female"],
                    title_args={"size":20},
                    anno_args={"rotation":0}, verbose=False, check=False)

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=True, anno_style="tight", titles=["Male","Female"], title_args={"size":20}, anno_args={"rotation":0}, verbose=False, check=False)

INFO:root:Extracted GTF attributes: ['gene_id', 'gene_name', 'gene_biotype']

Out[6]:

(<Figure size 3200x2400 with 6 Axes>, <gwaslab.g_Log.Log at 0x7fc603263f10>)

Note: Available since v3.4.47

In [7]:

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=12,
                    mode="r",
                    region_chromatin_files=["../examples/E098_15_coreMarks_mnemonics.bed.gz"],
                    region_chromatin_labels=["E098_15"],
                    cbar_fontsize=11,
                    marker_size=(100,100),
                    titles=["Male","Female"],
                    title_args={"size":20},
                    anno_args={"rotation":0,"fontsize":12}, 
                    verbose=False, check=False)

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=12, mode="r", region_chromatin_files=["../examples/E098_15_coreMarks_mnemonics.bed.gz"], region_chromatin_labels=["E098_15"], cbar_fontsize=11, marker_size=(100,100), titles=["Male","Female"], title_args={"size":20}, anno_args={"rotation":0,"fontsize":12}, verbose=False, check=False)

INFO:root:Extracted GTF attributes: ['gene_id', 'gene_name', 'gene_biotype']

Out[7]:

(<Figure size 3200x3200 with 7 Axes>, <gwaslab.g_Log.Log at 0x7fc603263f10>)

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