NAME

graph_profile.pl

A script to graph Y values along a genomic coordinate X-axis.

SYNOPSIS

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

OPTIONS

The command line flags and descriptions:

--in <filename>

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.

--index <index>

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.

--all

Automatically graph all available datasets present in the file.

--cen

Datasets should (not) be median centered prior to graphing. Useful when graphing multiple datasets together when they have different medians. Default is false.

--xindex <index>

Specify the column index of the X-axis dataset. Unless specified, the program automatically uses the columns labeled 'Midpoint' or 'Window', if present.

--skip <integer>

Specify the ordinal number of X axis major ticks to label. This avoids overlapping labels. The default is 1 (every tick is labeled).

--offset <integer>

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.

--xformat <integer>

Specify the number of decimal places the X axis labels should be formatted. The default is undefined (no formatting).

--min <number>

--max <number>

Specify the minimum and/or maximum values for the Y-axis. The default values are automatically determined from the dataset.

--yformat <integer>

Specify the number of decimal places the Y axis labels should be formatted. The default is undefined (no formatting).

--ytick <integer>

Specify explicitly the number of major ticks for the Y axes. The default is 8.

--color <name,name,...>

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.

--dir

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".

--version

Print the version number.

--help

Print this help documenation

DESCRIPTION

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.

AUTHOR

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 GPL (either version 1, or at your option, any later version) or the Artistic License 2.0.