baderlab / ccinx Goto Github PK

Hello,
I wanted to use the BuildGeneStatList() function, like below:

# Prepare for CCInx
gene_stats <- BuildGeneStatList(inD = sc_obj, cl = sc_obj$hpca_cell_name,
                                assayType = "", exponent = 2, pseudocount = 1)

But I am encountered with the following error:

Error in scClustViz::getExpr(inD, assayType) : assayType '' not found.
  The following assay data are available in this object:
  RNA, integrated

When I provide "RNA" as the assayType, I encounter the following error:

Error in scClustViz::getExpr(inD, assayType) : 
  argument "assaySlot" is missing, with no default

I am using the latest Seurat version:

> sc_obj@version
[1] ‘3.1.0’

I've also installed the latest scClustViz from Github:

# devtools::install_github('Baderlab/scClustViz')

Please let me know if I am doing anything incorrectly.

Thank you,
Farzan

Hello! Love this package. I just recently re-ran some analysis and am having some issue with ViewCCInx. BuildCCInx works fine, and I can get normal outputs. PlotCCInx still works.

Error seems to be in the Shiny app, after R updated.