DimPlot cannot color correctly

[liuweihanty]

Hi there, I was trying to use Dimplot to do a simple visualization of my data. The identity I used is a column called "label_coarse" stored in metadata, and is of data type "chr", I used the code below

Idents(seu.integrated) <- "label_coarse"
DimPlot(seu.integrated, group.by = "label_coarse",reduction = "umap"),

and the following error pops up:
Error: Must request at least one colour from a hue palette.

do you know how to resolve this? Thank you very much in advance!

[jaisonj708]

Please check to make sure all items in label_coarse have a value

[CarlottaHS]

Hi! I also run into the same error.

I am setting the Idents back to the originally created seurat_cluster column:
Idents(combined) <- "seurat_clusters"
DimPlot(object = combined, reduction = "umap")
Resulting in: ERROR while rich displaying an object: Error: Must request at least one colour from a hue palette.

I checked my meta.data columns or NA or empty entries:
allmisscols <- sapply(combined@meta.data, function(x) all(is.na(x) | x == '' ))
allmisscols
Resulting in:
orig.ident 0 nCount_RNA 0 nFeature_RNA 0 sampleName 0 percent.mt 0 RQ_GEX 0 area 0 disease 0 vaccine 0 RNA_snn_res.0.8 0 seurat_clusters 0 sub.cluster 0 cell_type 0 total_count 0 count_cell_type 0 frequency_cell_type 0 subject 0

So as far as I am aware my meta.data has no missing value.

Do you know how to resolve this?
Thanks already in advance!

[ncalistri]

Check to make sure that your Seurat object's metadata has retained the row names (should be cell barcode by default) as those are required for some Seurat plotting functions.

rownames(seurat_object@meta.data)

I've received a similar error message after manipulating the metadata data.frame, and found that I had accidentally converted it to a tibble and removed the rownames.

[KinSimon96]

Hey,

Facing the same problem, but only for violin plots. Did someone find the way to fix it ?

Thanks,
Simon

[CarlottaHS]

I solved the error in the same way as @ncalistri did.
Now I make sure to keep the row names in the object, when I manipulate the metadata. One has to be especially careful when using functions from the tidyverse suite as that then typically happens.

[AayushiNotra]

How do I fix missing values from my seurat meta data?