Miami plot

Implemented since v3.3.4

As a standalone function, GWASLab can plot Miami plot given a pair of sumstats files.

gl.plot_miami2()

gl.plot_miami2( 
          path1=None,
          path2=None,
          merged_sumstats=None,
          ...
          )

Updated since v3.4.38

GWASLab creates Miami plot by iteratively calling .plot_mqq(). The function name is plot_miami2() (not plot_miami()).

Options

Option	DataType	Description	Default
`path1`	`gl.Sumstats`	First sumstats object for top plot	`None`
`path2`	`gl.Sumstats`	Second sumstats object for bottom plot	`None`
`merged_sumstats`	`pd.DataFrame`	Merged sumstats DataFrame with suffixes (alternative to path1/path2)	`None`
`suffixes`	`list`	Suffixes for merged_sumstats columns (e.g., ["_1", "_2"])	`None`
`mode`	`string`	Plot mode: "m" (Manhattan only) or "mqq" (Manhattan + QQ)	`"m"`
`scaled`	`boolean`	Use MLOG10P for both plots	`False`
`scaled1`	`boolean`	Use MLOG10P for top plot	`False`
`scaled2`	`boolean`	Use MLOG10P for bottom plot	`False`
`id0`	`string`	ID column for merged_sumstats	`"TCHR+POS"`
`id1`	`string`	ID column for path1	`None`
`id2`	`string`	ID column for path2	`None`
`same_ylim`	`boolean`	Use same y-axis limits for both plots	`False`
`fig_kwargs`	`dict`	Arguments passed to plt.subplots()	`None`
`save`	`string` or `bool`	Save path or True for default path	`None`
`save_kwargs`	`dict`	Arguments passed to matplotlib savefig()	`None`
`fontsize`	`int`	Font size for labels	`10`
`font_family`	`string`	Font family	`"Arial"`
`dpi`	`int`	Dots per inch for figure	`100`
`verbose`	`boolean`	Print progress messages	`True`

gl.plot_miami2() supports most options from 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

Basic Miami plot

import gwaslab as gl

# Load two sumstats
gl1 = gl.Sumstats("sumstats1.tsv.gz", fmt="auto")
gl2 = gl.Sumstats("sumstats2.tsv.gz", fmt="auto")

# Create Miami plot
gl.plot_miami2(path1=gl1, path2=gl2)

Customized Miami plot with annotations

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,
    save="miami_plot.png",
    save_kwargs={"dpi": 300}
)

Using merged sumstats

# Merge two sumstats with suffixes
merged = gl.merge_sumstats([gl1, gl2], suffixes=["_1", "_2"])

# Create Miami plot from merged data
gl.plot_miami2(
    merged_sumstats=merged.data,
    suffixes=["_1", "_2"],
    id0="TCHR+POS"
)