Composite Plot

Generate a Composite Plot PNG from composite data like the output in TagPileup.

When reviewing the output from several TagPileup runs, this tool is convenient for the bulk visualization of these composite data.

The tool expects a text file with any extension formatted like the TagPileup's composite output of tab-delimited values with a single header column and the first row defining the domain:

<blank> -499    -498    -497    ... 499 500
Sample1_read1_sense.cdt 0.0 0.13333333333333333 0.0 0.0 ... 0.0 0.06666666666666667
Sample1_read1_anti.cdt  0.06666666666666667 0.0 0.0 ... 0.26666666666666666 0.0

The format allows for any number of rows and columns.

caution

Make sure the tab-delimited file has the same number of columns in each row. Differing number of values within each row will throw an error.

Include Legend

You may choose to include a legend for each heatmap which will specify which color was used for each row of the composite file with the name each row defined by the first column.

Image dimensions

The image height and width specify the number of pixels to squish or expand the numeric matrix into for the final output .png heat map image. Image dimensions are enabled with the selection of "Output Image."

Command Line Interface

Usage:

java -jar ScriptManager.jar figure-generation composite-plot [-hlV] [-o=<output>]
[-t=<title>] [-x=<pixelWidth>] [-y=<pixelHeight>] [-c=<colors>...]...
<compositeData>

Output Options

Option	Description
-o, --output=<output>	specify output filename, please use PNG extension (default=Input filename with "_compositePlot.png" appended to the name in working directory of ScriptManager

Plot Design Options

Option	Description
-t, --title=<title>	set title (default uses input file name)
-l, --legend	add a legend (default=no legend)
-x, --width=<pixelWidth>	indicate a pixel width for the plot (default=500)
-y, --height=<pixelHeight>	indicate a pixel height for the plot (default=270)
-c, --custom-colors=<colors>...	indicate colors to use for each series. Must indicate a number of colors that matches number of dataseries default behavior: if one series input, use black if two series input, use blue(sense) and red(anti) if greater than two series, cycle through a set of 20 preset colors.