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PlotGermline.md

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PlotGermline

PlotGermline will read one or more IMGT/IgBLASTPlus format files, and plot a histogram for each one, showing relative usage of the requested germline gene. If duplicate records have been consolidated, it can take account of a count in the ID field indicating the number of duplicates.

PlotGermline requires NumPy and matplotlib.

Usage

usage: PlotGermline.py [-h] [-a] [-b BARCOLOUR] [-c COLS] [-co] [-d DUPHEADER] [-f]
                       [-g] [-gh] [-gv GRID_VERTICAL] [-l LIMIT] [-s SAVE]
                       [-sz X,Y] [-t TITLES] [-w WIDTH] [-y YMAX]
                       infiles field detail
Argument Meaning
infiles Input file names, separated by commas (IMGT/IgBLASTPlus format.
field The germline field to analyse, e.g. 'V-GENE and allele'
detail F (family), G (germline) or A (allele) (this assumes naming similar to human germline genes: otherwise only A is supported)
[-a] Sort genes alphabetically in the plot (default is by decreasing usage)
[-b BARCOLOUR] Colours to use for plots (one or more colours, separated by commas). If there are more plots than colours, the colours will repeat in a cycle.
[-c COLS] Number of plots to place on each row of the output (default 1)
[-co] Consolidate statistics into a single plot or table
[-d DUPHEADER] Prefix of the duplicate count in the Sequence ID, e.g. 'DUPCOUNT='
[-f] Use frequency on the y-axis rather than number of reads
[-g] Fill bars with a gradiented colour (as in the example above)
[-gh] Show horizontal grid lines
[-gv GRID_VERTICAL] Show vertical grid lines after every GRID_VERTICAL number of bars
[-l LIMIT] Limit to the specified number of most frequently used genes
[-s SAVE] Save the plot to the specified file, otherwise display it interactively
[-sz X,Y] Set the total figure size to X by Y inches (note that the smaller the overall figure is, the larger the text is with respect to the plot, which gives some control over font size)
[-t TITLES] Comma-separated list of titles to use for plots (if there are fewer titles than plots, the titles will repeat in cycle)
[-w WIDTH] Column width, between 0 and 1 (0.8 in the above example)
[-y YMAX] Max y-value to use on all plots
[-h] Provide a help message and exit

Output Files

If the -s option is specified, the format will be determined by the extension of the specified output file(.pdf, .png, .jpg). If the extension is .csv, a csv file will be produced instead of a plot.

Testing

testfiles/Test_Commands.bat exercises the script with sample data.