object 'chans' not found while applying compensation

[cleanylee]

Hi @DillonHammill , thanks for the great package.

I tried to do compensation with the package and encountered some issues I couldn't figure out why. The error message happens when I tried to run cyto_plot_compensation or cyto_compensate

I followed the code of example article and also get the same error. (shown below)

Code:

The Console:

[williamsdrake]

Just ran into this problem as well. Following the vignette and sample data

> # Apply compensation
> gs <- cyto_compensate(gs,
+                       spillover = "Spillover-Matrix.csv")
Error in colnames(z) %in% chans : object 'chans' not found
> traceback()
6: colnames(z) %in% chans
5: which(!colnames(z) %in% chans)
4: FUN(X[[i]], ...)
3: lapply(spill, function(z) {
       cols_rm <- which(!colnames(z) %in% chans)
       if (length(cols_rm) > 0) {
           z <- z[, -cols_rm]
           row_rm <- LAPPLY(cols_rm, function(w) {
               which(z[, w] == 1)
           })
           row_rm <- row_rm[!is.na(row_rm)]
           if (length(row_rm) > 0) {
               z <- z[-row_rm, ]
           }
       }
       return(z)
   })
2: cyto_compensate.GatingSet(gs, spillover = "Spillover-Matrix.csv")
1: cyto_compensate(gs, spillover = "Spillover-Matrix.csv")

It appears the problem is within the function cyto_compensate.GatingSet.

[DillonHammill]

Apologies for not spotting this bug sooner, I have been working on getting the new version of CytoExploreR (v2.0.0) ready for release - if all goes to plan it should be available next week.

In the meantime, I have pushed a fix to the master branch on GitHub to fix this issue in version 1.1.0 of CytoExploreR. Please pull down the latest version from GitHub and let me know how you go.

devtools::install_github("DillonHammill/CytoExploreR")

[williamsdrake]

No need to apologize. It is working for me now after pulling the latest version. Just saw some tweets about v2, looking forward to it!

[cleanylee]

Thanks @DillonHammill It works perfectly now after the update. Looking forward to the new version !