manhattan_generator is a python tool to create beautiful Manhattan plots.
Here are the dependencies of the tool:
- Python version 2.7 or 3.4 or latest
- numpy version 1.8.0 or latest
- matplotlib version 1.3.1 or latest
- pandas version 0.17 or latest
We recommend installing the tool in a Python virtual environment.
manhattan_generator should work on Windows and MacOS, even though it hasn't
been fully tested for full compatibility.
$ manhattan_generator --help
usage: manhattan_generator [-h] [-v] [--twopoint FILE] [--multipoint FILE]
[--col-chr COL] [--col-name COL] [--col-pos COL]
[--col-cm COL] [--col-pvalue COL] [--col-lod COL]
[-o NAME] [-f FORMAT] [--web] [--dpi INT] [--bp]
[--use-pvalues] [--exclude-chr STRING]
[--no-negative-values] [--max-ylim FLOAT]
[--min-ylim FLOAT] [--no-y-padding]
[--graph-title TITLE] [--graph-xlabel TEXT]
[--graph-ylabel TEXT] [--graph-width WIDTH]
[--graph-height HEIGHT] [--point-size SIZE]
[--significant-point-size SIZE]
[--abline POS1,POS2,...]
[--significant-threshold FLOAT] [--no-annotation]
[--axis-text-size INT] [--chr-text-size INT]
[--label-text-size INT]
[--chromosome-box-color COLOR]
[--even-chromosome-color COLOR]
[--odd-chromosome-color COLOR]
[--multipoint-color COLOR]
[--significant-color COLOR]
This script produces nice Manhattan plots for either linkage or GWAS results.
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
Input Options:
Options for the input file(s) (name of the file, type of graph, etc.).
Note that for GWAS results, only the '--twopoint' option should be used.
--twopoint FILE The input FILE for two-point linkage.
--multipoint FILE The input FILE for multipoint linkage.
Column Options:
The name of the different columns in the input file(s).
--col-chr COL The name of the column containing the chromosomes
[Default: chr].
--col-name COL The name of the column containing the marker names
[Default: name].
--col-pos COL The name of the column containing the marker positions
[Default: pos].
--col-cm COL The name of the column containing the marker cM
[Default: cm].
--col-pvalue COL The name of the column containing the marker p values
[Default: p_value]
--col-lod COL The name of the column containing the marker LOD score
[Default: lod]
Graph Output Options:
Options for the ouput file (name of the file, type of graph, etc.).
-o NAME, --output NAME
The NAME of the ouput file [Default: manhattan].
-f FORMAT, --format FORMAT
The FORMAT of the plot (ps, pdf, png, eps) [Default:
png].
--web Always write a PNG file for web display, and return
the path of the PNG file.
--dpi INT The quality of the output (in dpi) [Default: 600].
Graph Options:
Options for the graph type (two-point, multipoint, etc.).
--bp Use physical positions (bp) instead of genetic
positions (cM).
--use-pvalues Use pvalues instead of LOD score. Requires to compute
-log10(pvalue).
--exclude-chr STRING Exclude those chromosomes (list of chromosomes,
separated by a coma) [Default: None].
Graph Presentation Options:
Options for the graph presentation (title, axis label, etc.).
--no-negative-values Do not plot negative values.
--max-ylim FLOAT The maximal Y value to plot [Default: maximum of
max(LOD) and 1+significant-threshold].
--min-ylim FLOAT The minimal Y value to plot [Default: -2.0].
--no-y-padding Do not add Y padding to the Y limit
--graph-title TITLE The TITLE of the graph [Default: empty].
--graph-xlabel TEXT The TEXT for the x label. [Default: Chromosome].
--graph-ylabel TEXT The TEXT for the y label. [Default: LOD].
--graph-width WIDTH The WIDTH of the graph, in inches [Default: 14].
--graph-height HEIGHT
The HEIGHT of the graph, in inches [Default: 7].
--point-size SIZE The SIZE of each points [Default: 2.1].
--significant-point-size SIZE
The SIZE of each significant points [Default: 4.5].
--abline POS1,POS2,...
The y value where to create a horizontal line,
separated by a comma [Default: 3,-2].
--significant-threshold FLOAT
The significant threshold for linkage or association
[Default: 3.0]
--no-annotation Do not draw annotation (SNP names) for the significant
results.
--axis-text-size INT The axis font size [Default: 12]
--chr-text-size INT The axis font size [Default: 12]
--label-text-size INT
The axis font size [Default: 12]
Graph Colors Options:
Options for the graph colors.
--chromosome-box-color COLOR
The COLOR for the box surrounding even chromosome
numbers [Default: #E5E5E5].
--even-chromosome-color COLOR
The COLOR for the box surrounding even chromosome
numbers [Default: #1874CD].
--odd-chromosome-color COLOR
The COLOR for the box surrounding odd chromosome
numbers [Default: #4D4D4D].
--multipoint-color COLOR
The COLOR for the multipoint plot [Default: #FF8C00].
--significant-color COLOR
The COLOR for points representing significant linkage
[Default: #FF0000].As an example, we used the dataset publicly provided by Wood et al. 2014 (doi: 10.1038/ng.3097], as part of the GIANT consortium for height (available here).
manhattan_generator \
--twopoint ../data/GIANT_HEIGHT_Wood_et_al_2014_publicrelease_HapMapCeuFreq.grch37.txt \
--col-chr Chromosome \
--col-name MarkerName \
--col-pos Position \
--col-pvalue p \
--bp \
--use-pvalues \
--abline 95 \
--significant-threshold 95 \
--no-annotation \
--significant-point-size 2 \
--point-size 1 \
--graph-title "GIANT height (Wood et al. 2014, public release)" \
--chr-text-size 10 \
--exclude-chr 23,24
