graph_profile.pl
A script to graph Y values along a genomic coordinate X-axis.
graph_profile.pl <filename>
Options: --in <filename> --index <index1,index2,...> --all --cen --xindex <index> --skip <integer> --offset <integer> --xformat <integer> --min <number> --max <number> --yformat <integer> --ytick <integer> --color <name,name,...> --dir <foldername> --version --help
The command line flags and descriptions:
Specify an input file containing either a list of database features or genomic coordinates for which to collect data. The file should be a tab-delimited text file, one row per feature, with columns representing feature identifiers, attributes, coordinates, and/or data values. The first row should be column headers. Text files generated by other BioToolBox scripts are acceptable. Files may be gzipped compressed.
Specify the column number(s) corresponding to the dataset(s) in the file to graph. Number is 0-based index. Each dataset should be demarcated by a comma. A range of indices may also be specified using a dash to demarcate the beginning and end of the inclusive range. Multiple datasets to be graphed together should be joined with an ampersand. For example, "2,4-6,5&6" will individually graph datasets 2, 4, 5, 6, and a combination 5 and 6 graph.
If no dataset indices are specified, then they may be chosen interactively from a list.
Automatically graph all available datasets present in the file.
Datasets should (not) be median centered prior to graphing. Useful when graphing multiple datasets together when they have different medians. Default is false.
Specify the column index of the X-axis dataset. Unless specified, the program automatically uses the columns labeled 'Midpoint' or 'Window', if present.
Specify the ordinal number of X axis major ticks to label. This avoids overlapping labels. The default is 1 (every tick is labeled).
Specify the number of X axis ticks to skip at the beginning before starting to label them. This may help in adjusting the look of the graph. The default is 0.
Specify the number of decimal places the X axis labels should be formatted. The default is undefined (no formatting).
Specify the minimum and/or maximum values for the Y-axis. The default values are automatically determined from the dataset.
Specify the number of decimal places the Y axis labels should be formatted. The default is undefined (no formatting).
Specify explicitly the number of major ticks for the Y axes. The default is 8.
Optionally specify the colors for the data lines. The default set is lred, lgreen, lblue, lyellow, lpurple, cyan, and lorange. See the documentation for GD::Graph::colour for a complete list.
Optionally specify the name of the target directory to place the graphs. The default value is the basename of the input file appended with "_graphs".
Print the version number.
Print this help documenation
This program will generate PNG graphic files representing a profile of values plotted along a specific X-axis. For example, plotting values along genomic coordinates or relative positions along a feature. The X-axis values are static and each dataset is plotted against it. One or more datasets may be plotted on a single graph, each in a different color, with a legend printed beneath the graph. The graph is a simple Bezier-smoothed line graph.
The resulting files are written to a subdirectory named after the input file. The files are named after the dataset name (column header) with a prefix.
Timothy J. Parnell, PhD Howard Hughes Medical Institute Dept of Oncological Sciences Huntsman Cancer Institute University of Utah Salt Lake City, UT, 84112
This package is free software; you can redistribute it and/or modify it under the terms of the Artistic License 2.0.
To install Bio::ToolBox, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::ToolBox
CPAN shell
perl -MCPAN -e shell install Bio::ToolBox
For more information on module installation, please visit the detailed CPAN module installation guide.