Plot the Q-score Heat map

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_qscore_heatmap 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-gc04a08b
 # Run Folder: 131212_221Bin1R0I
 set terminal png nocrop
 set output 'q_heatmap.png'
 set title "02D224DRR All Lanes"
 set yrange [0 : 45 ]
 set ylabel "Q Score"
 set xrange [0 : 31 ]
 set xlabel "Cycle"
 set view map
 plot "-" matrix with image
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0.017353 0.017634 0.0162293 0.019017 0.0131606 0.0134416 0.0162293 0.024895 0.0209836 0.0229501 0.0137009 0.019017 0.0162293 0.00922758 0.0243331 0 0.0380556 0.042248 0.0551277 0.0355272 0.0433718 0.437348 0.261354 1.08708 0

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.

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