plotFeatures and cellTopicHeatmap errors about cistopic

[cbravo93]

Hi,

Can you check colnames([email protected])?

Cheers,

C

[jk86754]

There is indeed no 'graphBasedClusters_CRA' in the colnames.

colnames([email protected])
[1] "nCounts" "nAcc" "10X_total" "10X_duplicate"
[5] "10X_chimeric" "10X_unmapped" "10X_lowmapq" "10X_mitochondrial"
[9] "10X_passed_filters" "10X_cell_id" "10X_is__cell_barcode" "10X_TSS_fragments"
[13] "10X_DNase_sensitive_region_fragments" "10X_enhancer_region_fragments" "10X_promoter_region_fragments" "10X_on_target_fragments"
[17] "10X_blacklist_region_fragments" "10X_peak_region_fragments" "densityClust"

I re-ran

cisTopicObject_d0 <- addCellMetadata(cisTopicObject_d0, graphBasedClusters_CRA_d0)

and now the colname does appear and cellTopicHeatmap works. Not sure why i had to add it again but it does work now :)

Still not sure about cellTopicHeatmap, though...

[cbravo93]

Can you check if the densityClust column is a factor?

[jk86754]

is.factor([email protected]$densityClust)
[1] TRUE

Thanks,

Joe

[JBreunig]

Just to chime in, I had the same problem, having to run "cisTopicObject_d0 <- addCellMetadata(cisTopicObject_d0, graphBasedClusters_CRA_d0)" twice.

To be fair, I never figured out exactly at which step the metadata got dropped but re-running that command always solved it.

[cbravo93]

May it be in this line (on the densityClust part)?

[email protected] <- [email protected][, -ncol([email protected])]

It is not made to be run, I added it for deleting the densityClust column when checking parameters, will take it out. For the error in cellTopicHeatmap, does it also occur when using the precomputed cisTopicObject?

Cheers,

C

[jk86754]

Thanks. If i can make densityClust work, cellTopicHeatmap works as well.