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guigolab / ggsashimi

Command-line tool for the visualization of splicing events across multiple samples
MIT License
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Colors not working #91

Closed naqvia closed 1 year ago

naqvia commented 2 years ago

I am trying to set the colors but it always seems to be grey (both groups). I have pasted the color palette, my bam file tsv, and command. 

ctrl    bams/6c37714d-e692-4982-a817-67818765a241.Aligned.out.sorted.bam    ctrl
tumor   bams/48645a9d-5f53-4db7-8b66-f0b0e5bbeb52.Aligned.out.sorted.bam    tumor
orange
cornflowerblue
docker run --platform linux/amd64 -w $PWD -v $PWD:$PWD guigolab/ggsashimi -b input_bams.tsv -c chr2:200853009-200864658 -g gencode.v33.annotation.transcr.gtf --shrink --alpha 0.15 --base-size=20 --ann-height=1.5 --height=3 --width=18 -P palette.txt

Am I doing something wrong?

bdgsilva commented 2 years ago

@naqvia, you need to use the parameter --color-factor with the number (1-based) of the column in your bam config file that specifies what you want to color (in your case, columns 1 or 3)

stale[bot] commented 1 year ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.