Turning off alignments when using the CLI

[kcleal]

I would like to use gw (current version 1.1.2) to plot static coverage images of numerous regions as part of an analysis pipeline. The individual command is created by the pipeline and dynamically altered based on the number of samples in a group, e.g.:

gw SILVA_cDNA.fa --theme igv --ylim 0 --cov 150 -n --fmt png -f '../NEB_S1_SILVA_138_SSURef_NR99_AK059639_1_1307.png' --dims '1307x1800' --region 'SILVA_138_SSURef_NR99;AK059639.1.1307:1-1307' --bam P30602_201_S1.rrna.bam --bam P30602_202_S2.rrna.bam --bam P30602_203_S3.rrna.bam --bam P30602_204_S4.rrna.bam --bam P30602_205_S5.rrna.bam --bam P30602_206_S6.rrna.bam --bam P30602_207_S7.rrna.bam --bam P30602_208_S8.rrna.bam --bam P30602_209_S9.rrna.bam --bam P30602_210_S10.rrna.bam --bam P30602_211_S11.rrna.bam --bam P30602_212_S12.rrna.bam

The goal is to plot the coverage of numerous samples in a small region (just 1000-5000bp). Using '--ylim 0 --cov 150’, I seem to have been able to suppress plotting the single alignments and showing the coverage only. However, the browser still seems to reserve that space, ultimately leading to excessive whitespace in the better part of the image:

My script is smart enough to alter the --dims ‘1307x1800’ according to the number of samples and the size of the region to be plotted (currently set to 1px per bp in x and 150px per sample in y), but I fail to get rid of that whitespace.

Am I overlooking a CLI argument or do you perhaps have another suggestion?

Matthias Zepper

[kcleal]

Hi Matthias,

I can see what you are trying to do, but setting ylim 0 does not turn off reserving space for alignments - I think this is a bug, and it should work the way you are trying. However, there is another way to get the desired effect, simply use the --command option available on the CLI, this will apply a command right before any drawing commands are issued. For example:

gw hg38 -b ./DB53.bam -b ./DB53.bam -b ./DB53.bam --command "alignments" --command "load ideogram hg19" -n -r chr1:1-20000 > test.png

This is the same as running the alignments command followed by load ideogram hg19 (the alignments command toggles alignments on/off, as they are on by default, this will toggle them off!)

[MatthiasZepper]

Thank you very much! That did the trick!