使用plink assoc输出绘制曼哈顿图和QQ图。
qqman的Python项目详细描述
Python的qqman
如果您想查看源代码或有任何问题，请在我的github存储库中留言。
这个库的灵感来自r-qqman（参见here）。
它还包含/将包含python用户的其他方法。
目录
- Introduction
1.1条。Installation
1.2条。Requirements
1.3条。Features - Manhattan Plot
2.1条。Parameters
2.2条。Examples - QQ Plot
3.1条。Parameters
3.2条。Examples
1. Introduction
1.1. Installation
使用pip
$ pip install qqman
1.2. Requirements
- matplotlib库
- 熊猫
- numpy公司
pip
^{pr2}$阿南科达
$ conda install -c anaconda numpy $ conda install -y -c anaconda pandas $ conda install -y -c conda-forge matplotlib
1.3. Features
2. Manhattan Plot
从PLINK（assoc输出或包含[染色体/基对/p值]作为列的任何assoc格式的数据绘制曼哈顿图。在
2.1. Parameters
|
^{ |
- Input file path and name of the Plink assoc output. - Pandas DataFrame with columns [chromosome/basepair/p-value] |
|---|---|
| ^{ ( optional ) | Output path and file name of the plot. (ie. out="./Manhattan.png") |
| ^{ ( optional : default=Greys_r ) | A Colormap instance or registered colormap name. matplotlib.cm.get_cmap() |
| ^{ ( optional : default=2 ) | int : Number of colors to use list : Specific colors to use in colormap |
| ^{ ( optional ) | If true, the plot will be shown on your screen. (This option doesn't work in CUI environment.) |
| ^{ ( optional : default=10) | A size of gaps between the group of scatter markers of each chromosome in Manhattan plot |
| ^{ ( optional ) | If given, this subplot is used to plot in instead of a new figure being created. |
| ^{ ( optional ) | A title of the plot. |
| ^{ ( optional ) | A size of the title of the plot. |
| ^{ ( optional ) | A size of x and y labels of the plot. |
| ^{ ( optional ) | A size of xtick labels. |
| ^{ ( optional ) | A size of ytick labels. |
| ^{ ( optional ) | A rotation degree of xtick labels. |
| ^{ ( optional ) | A rotation degree of ytick labels. |
| ^{ ( optional : default="CHR" ) | A string denoting the column name for the chromosome. Defaults to PLINK’s "CHR" Said column must be numeric. If you have X, Y, or MT chromosomes, be sure to renumber these 23, 24, 25, etc. |
| ^{ ( optional : default="BP" ) | A string denoting the column name for the chromosomal position. Defaults to PLINK’s "BP" Said column must be numeric. |
| ^{ ( optional : default="P" ) | A string denoting the column name for the p-value. Defaults to PLINK’s "P" Said column must be numeric. |
| ^{ ( optional : default="SNP" ) | A string denoting the column name for the SNP name (rs number). Defaults to PLINK’s "SNP" Said column should be a character |
| ^{ ( optional : default=-log_10(1e-5) ) | Where to draw a "suggestive" line. Set to False to disable. |
| ^{ ( optional : default=-log_10(5e-8) ) | Where to draw a "genome-wide sigificant" line. Set to False to disable. |
2.2. Examples
2.2.1。简单
fromqqmanimportqqmanif__name__=="__main__":qqman.manhattan("../../temp.assoc",out="./Manhattan.png")
2.2.2条。使用子批次
fromqqmanimportqqmanimportpandasaspdimportmatplotlib.pyplotaspltif__name__=="__main__":df_assoc=pd.read_csv("../../temp.assoc",header=0,delim_whitespace=True)figure,axes=plt.subplots(nrows=2,ncols=2,figsize=(20,20))qqman.manhattan("../../temp.assoc",ax=axes[0,0],title="Wider gap 100",gap=100)qqman.manhattan("../../temp.assoc",ax=axes[0,1],title="No lines",suggestiveline=False,genomewideline=False)qqman.manhattan("../../temp.assoc",ax=axes[1,0],title="Different colormap",cmap=plt.get_cmap("jet"),cmap_var=10)qqman.manhattan(df_assoc,ax=axes[1,1],title="From DataFrame with xtick rotation",xrotation=45)figure.tight_layout()plt.savefig("./manhattan.png",format="png")plt.clf()plt.close()
3. QQ Plot
从GWAS的p值绘制分位数-分位数图。在
3.1. Parameters
^{tb2}$3.2. Examples
3.2.1。简单
fromqqmanimportqqmanif__name__=="__main__":qqman.qqplot("../../temp.assoc",out="./QQplot.png")
3.2.2。使用子批次
fromqqmanimportqqmanimportpandasaspdimportmatplotlib.pyplotaspltif__name__=="__main__":df_assoc=pd.read_csv("../../temp.assoc",header=0,delim_whitespace=True)p_vals=list(df_assoc['P'])figure,axes=plt.subplots(nrows=2,ncols=2,figsize=(20,20))qqman.qqplot("../../temp.assoc",ax=axes[0,0],title="From file")qqman.qqplot(p_vals,ax=axes[0,1],title="From list")qqman.qqplot(df_assoc.P,ax=axes[1,0],title="From Series")qqman.qqplot(df_assoc,ax=axes[1,1],title="From DataFrame")figure.tight_layout()plt.savefig("./SubQQplot.png",format="png")plt.clf()plt.close()
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