Hi, I’m very new to using graphlan. I have a cladogram that was generated with lefse using the Galaxy website. I’ve been asked to format this cladogram a bit differently using graphlan. I’ve installed both export2graphlan v0.22 and graphlan v1.1.3 on a system running Rocky Linux 8.9. I’m not having any issue generating a cladogram, but I can’t change the background (shaded area) colors using the background_annotation_parameter either with export2graphlan or graphlan. Colors always default to green and blue for the background shading. I see there is a way to manually adjust colors in the annotation file, however this will be a tedious process so I was wondering if there’s a quicker way around it. Or, is there a way to turn off the annotation shading altogether? I may be misunderstanding which parameter controls the shaded areas and/or how to modify it.
# I want shaded areas of red and green instead of green and blue
export2graphlan.py -o vancPostNeoPost_lefseInput.res -t tree_1.txt -a annotations_1.txt --annotations 2 --external_annotations 3,4,5 --background_colors "#cc0000, #38761d"
graphlan_annotate.py --annot annotations_1.txt tree_1.txt tree_2.txt
graphlan.py tree_2.txt tree_2.pdf --format pdf
Any help is appreciated.
Thanks, R