R is very new to me. I try to make a DotPlot. Here is my code: ...
Idents(immune.combined) <- factor(Idents(immune.combined), levels = c("HSPC", "Mono/Mk Doublets",
"pDC", "Eryth", "Mk", "DC", "CD14 Mono",
"CD16 Mono", "B Activated", "B",
"CD8 T", "NK", "T activated",
"CD4 Naive T", "CD4 Memory T"))
Idents(immune.combined)
markers.to.plot <- c("CD3D", "CREM", "HSPH1", "SELL", "GIMAP5", "CACYBP", "GNLY", "NKG7", "CCL5",
"CD8A", "MS4A1", "CD79A", "MIR155HG", "NME1", "FCGR3A", "VMO1", "CCL2", "S100A9", "HLA-DQA1",
"GPR183", "PPBP", "GNG11", "HBA2", "HBB", "TSPAN13", "IL3RA", "IGJ", "PRSS57")
DotPlot(immune.combined, features = markers.to.plot, cols = c("blue", "red"), dot.scale = 8, split.by = "condition") + RotatedAxis()
Than I got this error/ warnings: Warning: Found the following features in more than one assay, excluding the default. We will not include these in the final data frame: CD3D, HSPH1, GNLY, NKG7, CCL5, CD8A, MS4A1, CD79A, NME1, FCGR3A, VMO1, S100A9, HLA-DQA1, GPR183, PPBP, GNG11, HBB, TSPAN13, IL3RA, PRSS57 Warning: Could not find CREM in the default search locations, found in RNA assay instead Error in intI(j, n = d[2L], dn[[2L]], give.dn = FALSE) : ungültige Zeichenindexierung In addition: Warning message: In cells.idents["NA"] <- names(x = which(x = is.na(x = Idents(object = object)[cells]))) : number of items to replace is not a multiple of replacement length
can anybody help me? I really would appreciate this. Greets
I tried to google this problem and try with chatGPT, but this wasn´t helpful.
