This application writes out a file that is compatible with both TSV (tab separated values) and GNUPlot, a command line plotting tool available on Linux, Mac OSX and Windows.

Running the Program

The program runs as follows:

 $ plot_by_cycle 140131_1287_0851_A01n401drr

In this sample, 140131_1287_0851_A01n401drr is a run folder and the summary is written to the standard output.

 # Version: v1.0.4-147-gb6d5c19-dirty
 # Run Folder: 1177190_11618Unbin2R1I
 set terminal png nocrop
 set output 'plot_by_cycle.png'
 set title "000000000-A1W6M All Lanes Channel A All Surfaces"
 set yrange [0 : 850.85 ]
 set ylabel "Intensity"
 set xrange [0 : 80 ]
 set xlabel "Cycle"
 plot "-" using 1:3:2:6:5 with candlesticks notitle lt rgb "black" whiskerbars
 1  98.5    106 109 111 118.5
 2  83.5    103 110 116 135.5
 3  87  102 107 112 127
 e

Available Options

The following options are supported in addition to the run folder. They must be given in the form: --filter-by-lane=1 with no additional space between the option name and value.

Metric Options

--metric-name=<name>: Metric to plot

Filter Options

--filter-by-lane=<lane number>: Only the data for the selected lane will be displayed
--filter-by-channel=<channel number>: Only the data for the selected channel will be displayed
--filter-by-base=<(A,C,G,T)>: Only the data for the selected base will be displayed
--filter-by-surface=<surface number>: Only the data for the selected surface will be displayed
--filter-by-read=<read number>: Only the data for the selected read will be displayed
--filter-by-cycle=<cycle number>: Only the data for the selected cycle will be displayed
--filter-by-lane=<lane number>: Only the data for the selected lane will be displayed
--filter-by-tile-number=<tile number>: Only the data for the selected tile number will be displayed
--filter-by-swath=<swath number>: Only the data for the selected swath will be displayed
--filter-by-section=<section number>: Only the data for the selected section will be displayed