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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()

gl.plot_miami( 
          path1,
          path2,
          ...
          )

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/)