Tom Carroll

Also had a simliar issue, but now fixed with the update to 2.23.6, i.e. `BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")`. Thanks for the workaround @g27182818 and the quick update @tiagochst!

> I had the same problem with ”Some values were outside the colour scale and will be treated as NA”. I used color_cells_by = "cell.type" ), only return blank trajectory....

Hey there @koldam, glad it helped! I made another quick tweak in another branch so it should work for more than 8 colors now by default. I haven't tested it...

also @koldam @jietian-327 were the colData columns you passed to color_cells_by character vectors or factors? i.e. if you passed cell.type, does `class(cds@colData$cell.type)` return character or factor? Just narrowing this down...

Great, glad that's helped @koldam! have merged those changes into my master branch now, so plain old `devtools::install_github("t-carroll/monocle3")` should work for anyone else having these issues. For the gene-cluster heatmap,...

Hi @ctrapnell @brgew @hpliner- If helpful, I have made some minor tweaks to plot_cells_3d to address an issue a few of us were having with passing factors from colData to...

Same issue here with the Docker image on Windows- anyone been able to resolve this?

Stared more closely at the console output during the various package installations and was able to find the problem in my case: R package xml2 fails to install. devtools needs...

I also have this issue- would be great if there could be a conda option as an alternative, or some other prescribed way to install required dependencies.

> I did it following the dockerfile. In fact ,I dont run with any AWS S3 inputs or outputs,so the boto3 package is not necessary and the corresponding code in...