Plot by lane

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_by_lane 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: 11115124_11854Unbin2R2I
 set terminal png nocrop
 set output 'plot_by_lane.png'
 set title "000000000-ABWLV"
 set yrange [0 : 1528.36 ]
 set ylabel "Density (K/mm2)"
 set xrange [0 : 2 ]
 set xlabel "Lane"
 plot "-" using 1:3:2:6:5 with candlesticks title "Density (K/mm2)" lt rgb "blue" whiskerbars ,"-" using 1:3:2:6:5 with candlesticks title "PF" lt rgb "dark-green" whiskerbars
 1  1164.6  1205.49 1218.97 1232.75 1273.63
 e
 1  955.386 1015.23 1036.47 1055.12 1114.97
 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