This application writes out of 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_flowcell 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 'flowcell.png'
 set title "000000000-A1W6M Intensity"
 set view map
 unset key
 unset tics
 unset border
 set cbrange [103:116]
 set palette defined (0 "blue", 0.33 "green", 0.66 "yellow", 1 "orange")
 plot "-" matrix with image
 104 110
 106 105
 105 104
 108 103
 111 106
 115 108
 109 106
 113 108
 116 108
 116 107
 114 109
 111 110
 116 109
 116 111

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