search

diazlab / CONICS

CONICS: COpy-Number analysis In single-Cell RNA-Sequencing
73 stars 28 forks source link

error on "plotChromosomeHeatmap" function within 10x scRNA data #7

Closed helianthuszhu closed 5 years ago

helianthuszhu commented 5 years ago

Hi, CONICSmat is a great package I am trying to using to visualize cnv from my 10x scRNA data. Here is issue I got when I ran "CONICSmat" using my own data.

plotChromosomeHeatmap(dat, normal = normal, plotcells = which(patients=="cluster_1"), gene_pos = gene_pos, windowsize = 121, chr=T,expThresh=0.4, thresh = 1) [1] "Generating distance Matrix" Error in apply(d, 2, function(x) x - mean(x)) : dim(X) must have a positive length Can anyone explain this for me or give me any suggestions how to figure it out? Thanks.

helianthuszhu commented 5 years ago

Oh, I have found my plotcells parameter was wrong before. In my case, I also got the WGS data to visualize the cnv, however, compared with the output of CONICSmat, some of the cnv regeion is not consistent. Could you guys have any advices to adjust the 10x scRNA data within CONICSmat?