Generate a manhattan plot given a file with (at least) chromosome, x, p-value. Offers a number of command-line options and the code is simple enough that it can be further customized.
The input file(s) (or stdin via -) can be in any format but the user must specify which columns to extract for chr, x, p using the --cols parameter.
Usage:
manhattan-plot.py [options] files
plot a manhattan plot of the input file(s).
Options:
-h, --help show this help message and exit
--no-log don't do -log10(p) on the value
--cols=COLS zero-based column indexes to get chr, position, p-value
respectively e.g. 0,1,2
--colors=COLORS cycle through these colors
--image=IMAGE save the image to this file. e.g. manhattan.png
--title=TITLE title for the image.
--ymax=YMAX max (logged) y-value for plot
--sep=SEP data separator, default is [tab]
--lines plot the p-values as lines extending from the x-axis rather
than points in space. plotting will take longer with this
option.
a command like:
$ python manhattan-plot.py --cols 0,1,6 input.bed
generates
there are a number of options, including adding custom colors.
$ python manhattan-plot.py --colors rgbk --cols 0,1,6 input.bed --image manhattan.rgbk.png
generates
