search

akdess / CaSpER

77 stars 28 forks source link

plotHeatmap function can only show cell ids instead of patient ids (group names) #77

Open lifan18 opened 2 years ago

lifan18 commented 2 years ago

Dear all,

Does anyone know how these codes in the demo (https://github.com/akdess/CaSpER/blob/master/demo/sCellGBM.R) show the patient ids (not cell ids) as it shows in Nature communication paper (https://www.nature.com/articles/s41467-019-13779-x#MOESM1)？

In the demo
## plot median filtered gene expression matrix 
plotHeatmap(object, fileName="heatmap.png", cnv.scale= 3, cluster_cols = F, cluster_rows = T, show_rownames = T, only_soi = T)

How did this plot out as the color codes represent the patient id?

image 
In the demo
## plot large scale events using event summary matrix 1: amplification, -1:deletion, 0: neutral
plotLargeScaleEvent2 (finalChrMat, fileName="large.scale.events.summarized.pdf")

How did this also plot out as the color codes represent the patient id?

image

In my case following the demo codes it only shows all cell ids:(

image

Hope anyone can figure it out.

Thank you for any help in advance!

Best

twoneu commented 1 year ago

I'm also curious about the patient-level groupings - @lifan18 did you happen to figure it out?