nelnour/capsule

An R package that visualizes Human Cell Atlas annotations on an SVG cell image.

capsule's Issues

Error after running `whereIs`

Not sure what is happening but this error occurs only after the command.

   > whereIs("DVL2", enhanced)
    Error in if (grep(";", as.character(HPASet[hgnc_symbol, ]$Loci))) { : 
        argument is of length zero

Python port?

Thanks for your repo. I was wondering if you have or know, a package similar to yours, ported to python?

What does it mean if other genes can't generate plot?

As from testing, only DVL2 was able to generate plot of cell.

> whereIs("ZSCAN1", enhanced, "Approved")
 Error in `[.data.frame`(HPASet[hgnc_symbol, ], reliability) : 
undefined columns selected 
> whereIs("XRCC4", enhanced, "Enhanced")
Error in if (grep(";", as.character(HPASet[hgnc_symbol, ][reliability])) >  : 
  argument is of length zero
> whereIs("HCCS", enhanced, "Enhanced")
Error in if (grep(";", as.character(HPASet[hgnc_symbol, ][reliability])) >  : 
  argument is of length zero
> 

Infinite install of BiocManager

Latest release had made these lines do infinite loops.

I was doing the source.

> install.packages("BiocManager")
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/BiocManager_1.30.17.tgz'
Content type 'application/x-gzip' length 352204 bytes (343 KB)
==================================================
downloaded 343 KB


The downloaded binary packages are in
	/var/folders/tj/6pskj5gs1fbg6gb02v4q1s_r0000gn/T//RtmpslL6SS/downloaded_packages
> source("./inst/scripts/scriptTemplate.R")
Bioconductor version 3.15 (BiocManager 1.30.17), R 4.2.0 (2022-04-22)
Error in install.packages : Updating loaded packages
> install.packages("BiocManager")
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/BiocManager_1.30.17.tgz'
Content type 'application/x-gzip' length 352204 bytes (343 KB)
==================================================
downloaded 343 KB


The downloaded binary packages are in
	/var/folders/tj/6pskj5gs1fbg6gb02v4q1s_r0000gn/T//RtmpslL6SS/downloaded_packages
> install.packages("BiocManager")
Error in install.packages : Updating loaded packages
> install.packages("BiocManager")
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/BiocManager_1.30.17.tgz'
Content type 'application/x-gzip' length 352204 bytes (343 KB)
==================================================
downloaded 343 KB


The downloaded binary packages are in
	/var/folders/tj/6pskj5gs1fbg6gb02v4q1s_r0000gn/T//RtmpslL6SS/downloaded_packages
> source("./inst/scripts/scriptTemplate.R")
Error in install.packages : Updating loaded packages

Restarting R session...

> install.packages("BiocManager")
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/BiocManager_1.30.17.tgz'
Content type 'application/x-gzip' length 352204 bytes (343 KB)
==================================================
downloaded 343 KB


The downloaded binary packages are in
	/var/folders/tj/6pskj5gs1fbg6gb02v4q1s_r0000gn/T//Rtmp2MOeJI/downloaded_packages
> ```