Profile: Bar graph of relationships(s) per position

Profile: Input files

You can give any number of positional table files:

relate-per-pos.csv
mask-per-pos.csv
clust-per-pos.csv

See General parameters for graphing: Input files for more information on input files.

Profile: Settings

See General parameters for graphing: Input data for more information on graph options.

Profile: Output files

See General parameters for graphing: Output files for more information on output files.

Profile: Examples

Assume your output files are in the directory out.

Graph the fraction of reads mutated (the mutation rate) at each position

Command:

seismic graph profile out

Outputs:

out/{sample}/graph/{ref}/{sect}/profile_masked_m-ratio-q0.csv
Position,Base,Mutated
196,A,0.03212678813091909
197,C,0.003393658868599399
198,A,0.010770982726367673
199,G,
200,T,
...
out/{sample}/graph/{ref}/{sect}/profile_masked_m-ratio-q0.html

Graph the fraction each type of mutation at each position

Command:

seismic graph profile -r acgtdi out

Outputs:

out/{sample}/graph/{ref}/{sect}/profile_masked_acgtdi-ratio-q0.csv

Position,Base,Subbed-A,Subbed-C,Subbed-G,Subbed-T,Deleted,Inserted
196,A,0.0,0.018827932574530207,0.0016602828354697209,0.011638240863466542,0.0,0.0
197,C,0.0012500543750758389,0.0,0.00042715097170304697,0.0017164535218205134,0.0,0.0
198,A,0.0,0.002887023310345601,0.0005903400048243549,0.007293619411197718,0.0,0.0
199,G,,,,,,
200,T,,,,,,
...

out/{sample}/graph/{ref}/{sect}/profile_masked_acgtdi-ratio-q0.html

Graph the number of informative reads at each position

Command:

seismic graph profile -r n --use-count out

Outputs:

out/{sample}/graph/{ref}/{sect}/profile_masked_n-count.csv
Position,Base,Informed
196,A,301334.2
197,C,305746.7
198,A,303045.7
199,G,
200,T,
...
out/{sample}/graph/{ref}/{sect}/profile_masked_n-count.html