Miami plot
Implemented since v3.3.4
As a standalone function, GWASLab can plot Miami plot given a pair of sumstats files.
gl.plot_miami()
Updated since v3.4.38
GWASLab creates Miami plot by iteratively calling .plot_mqq()
.
Options
Option | DataType | Description | Default |
---|---|---|---|
path1 |
gl.Sumstats |
gl.Sumstats Object | - |
path2 |
gl.Sumstats |
gl.Sumstats Object | - |
gl.plot_miami()
now supports most options in plot_mqq()
.
- Add a suffix "1" to the options and it will be passed to the top Manhattan plot.
- Add a suffix "2" to the options and it will be passed to the bottom Manhattan plot.
- If no suffix is provided, it will be passed to both plots.
Example
Example
``` gl.plot_miami2(path1= gl1, path2= gl2, skip=2, cut1=20, cut2=15, id1="SNPID", id2="SNPID", anno1=True, anno2="GENENAME", additional_line1=[1e-14], anno_set1=["rs3798519"], pinpoint1=[["rs3798519","rs35560038"],["rs7933262","rs8098510"]], pinpoint_color1=["purple","black"], highlight1=["rs8098510"], highlight2=[["rs8098510","rs3798519"], ["rs1491850"]], highlight_color2=["red","yellow"], jagged=True, verbose1=False, verbose2=False
) ```
See [Miami plot](https://cloufield.github.io/gwaslab/visualization_miami2/)