Simple but customisable beanplots from the command-line via python.
Generally speaking you only need a working Python installation and some common python libraries. This script was developed using Python 2.7.3.
Local install: Put this script in the direction where you want to use it and make it executable.
Global install: Make the script executable and copy it to a directory that is in your PATH variable (e.g. ~/bin):
$ chmod u+x beanplot
$ cp beanplot ~/bin
#test
$ beanplot -h- matplotlib
- scipy.stats
- numpy
$./beanplot -h
usage: beanplot [-h] [-v] [-o STRING] [-d STRING] [-a] [-c INT [INT ...]]
[-y STRING] [-x STRING] [--xmax FLOAT] [--xmin FLOAT]
[--ymax FLOAT] [--ymin FLOAT] [--turn] [--fontsize INT]xs
[--linewidthaxis INT] [--connect STRING] [--pheight FLOAT]
[--pwidth FLOAT] [--noOverallMean] [--overallMedian]
[--noStrips] [--noMeans] [--noMedians]
[--stripColor HTMLCOLORCODE]
[--medianMarkerColor HTMLCOLORCODE]
[--meanStripColor HTMLCOLORCODE] [--violinColor HTMLCOLORCODE]
[--multiplecolors COLORMAP]
FILE
Beanplot for each column of a file.
positional arguments:
FILE Delimited file. [if set to "-" or "stdin" reads from
standard in]
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
-o STRING, --out STRING
Outfile. File-ending determines outfile-type, e.g.
seb.pdf, will create a PDF.[If not set, interactive
mode enabled.]
-d STRING, --delimiter STRING
Delimiter used in file. [default: "tab"]
-a, --header Header in File. Header values will be variable names
for each beanplot. [Default: False]
-c INT [INT ...], --columns INT [INT ...]
Columns to exclude.
Plot:
General plotting arguments:
-y STRING, --ylabel STRING
y-label for the beangraph.
-x STRING, --xlabel STRING
x-label for the beanplot.
--xmax FLOAT x-axis maximum limit.
--xmin FLOAT x-axis minimum limit.
--ymax FLOAT y-axis maximum limit.
--ymin FLOAT y-axis minimum limit.
--turn Turn x-ticklabels by 90 degree to make them readable.
--fontsize INT Font-size. [default: 14]
--linewidthaxis INT Font-size of axis line-width. [default: 2]
--connect STRING HTML-color code,transparency-level to use to connect
row-elements to generate line-plot on top of beanplot.
e.g. "#A4A4A4,0.15" [default: None]
--pheight FLOAT Set the picture-height in inches. [default: 4.]
--pwidth FLOAT Set the picture-width in inches. [default: 6.]
Beanplot:
Beanplot specific arguments:
--noOverallMean Turn off overall mean line.
--overallMedian Turn on overall median line. [Default: OFF]
--noStrips Turn off striplines lines.
--noMeans Turn off individual mean lines.
--noMedians Turn off individual median points.
--stripColor HTMLCOLORCODE
Set strip color [default: #FFFFFF (white)]
--medianMarkerColor HTMLCOLORCODE
Set median marker color [default: #FFFFFF (white)]
--meanStripColor HTMLCOLORCODE
Set mean strip color [default: #FFFFFF (white)]
--violinColor HTMLCOLORCODE
Set violin color [default: #3366CC (blue)]
--multiplecolors COLORMAP
Colormap (pylab.cm) for plotting violin colors, e.g
winter, summer, autumn, rainbow, etc. [default: None].
Examples of possible colormaps here: http://wiki.scipy
.org/Cookbook/Matplotlib/Show_colormaps
Copyright Sebastian Schmeier (s.schmeier@gmail.com)
Basic beanplot for a tab-separated file with stripchart, one-colored violinplots, dotted line indicating overall mean, white dots indicating individual medians, and longer strips for individual means.
$ cat test_data.txt | tail -n +2 | ./beanplot - -o test_data1.png
First row in the file is a header, use header labels as tick-labels and turn them 90 degree to make them readable, use a matplotlib colormap for creating different colors for each beanplot. Set a y-label.
$ ./beanplot test_data.txt -a --turn --multiplecolors summer --ylabel Expression -o test_data2.png
Different colormap, make font bigger, remove stripchart, means and medians.
$ ./beanplot test_data.txt -a --turn --multiplecolors autumn --ylabel Expression --fontsize 22 -o test_data3.png --noOverallMean --noStrips --noMeans --noMedians
Reading data from stdin. Connect row-elements with a line using the --connect argument. It expects a HTML-color and a transparency-level. This might be useful for connecting e.g. time-course data like in this example.
$ cat test_data.txt | cut -f 1-6 | ./beanplot - -a --turn --multiplecolors Reds_r --ylabel Expression --connect "#A4A4A4,0.2" -o test_data4.png
- 0.1.7 2015/09/25 Cleaned code-base.
- 0.1.6 2014/10/08 Added possibility to change the color of the mean strips.
- 0.1.5 2014/09/01 Added possibility to connect row-elements trough a line.
- 0.1.4 2014/08/28 Made x and y axes limits adjustable.
- 0.1.3 2014/08/28 Small bug-fix of x-label display.
- 0.1.2 2014/07/31 Working version.
- 0.1 2014/06/04 Initial version.