Coloring not working for TSNE and UMAP plots for option color by = "Cluster"

[IkjotSidhu]

Coloring by the cluster is not working for umap and tsne plots-

> cluster.plot(my.obj,plot.type = "umap",interactive = F)

Error: Aesthetics must be either length 1 or the same as the data (36689): colour

> cluster.plot(my.obj,plot.type = "umap",interactive = F,col.by="clusters")

Error: Aesthetics must be either length 1 or the same as the data (36689): colour

[rezakj]

Run clustering and UMAP again and see if you get an error. Also update iCellR from CRAN.

library(devtools)
install_github("rezakj/iCellR")

Then:

# quick example 
library(Rphenograph)
my.obj <- run.phenograph(my.obj, k = 100, dims = 1:10)

my.obj <- run.umap(my.obj, dims = 1:10, method = "umap-learn") 

Let me know if this didn't help.

[IkjotSidhu]

I am getting an error while trying to install another required package called - digest.

• installing source package ‘digest’ ... package ‘digest’ successfully unpacked and MD5 sums checked libs g++ -std=gnu++11 -I"/gpfs/share/apps/R/3.5.1/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c SpookyV2.cpp -o SpookyV2.o gcc -I"/gpfs/share/apps/R/3.5.1/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c aes.c -o aes.o gcc -I"/gpfs/share/apps/R/3.5.1/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c crc32.c -o crc32.o gcc -I"/gpfs/share/apps/R/3.5.1/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c digest.c -o digest.o digest.c: In function ‘vdigest’: digest.c:475:9: error: ‘for’ loop initial declarations are only allowed in C99 mode for (R_xlen_t i = 0; i < n; i++){ ^ digest.c:475:9: note: use option -std=c99 or -std=gnu99 to compile your code digest.c:480:9: error: ‘for’ loop initial declarations are only allowed in C99 mode for (R_xlen_t i = 0; i < n; i++){ ^ make: *** [digest.o] Error 1 ERROR: compilation failed for package ‘digest’
• removing ‘/gpfs/data/feskelab/R/x86_64-pc-linux-gnu-library/3.5/digest’ Error: Failed to install 'Rphenograph' from GitHub: (converted from warning) installation of package ‘digest’ had non-zero exit status

[IkjotSidhu]

I think that I found the cause of the error. It seems that even after performing batch correction using MNN and Running dimensionality reduction, the object does not contain cluster information.

[rezakj]

Yes, you would need to run clustering after batch correction.