plotGroups HOW TO ORDER CLUSTER

[A-legac45]

HELLO,

in plotGroups how to order clusters for example

p4 <- plotGroups(
ArchRProj = proj,
groupBy = "new_cluster_namesatac_janv",
colorBy = "cellColData",
name = "log10(nFrags)",
plotAs = "violin",
alpha = 0.4,
baseSize = 10,
addBoxPlot = TRUE, pal = color_atac
)

give C1 C2 C3

and I would like C2 C3 C1

Thanks

[Zepeng-Mu]

Can you try making new_cluster_namesatac_janv a factor (factor(new_cluster_namesatac_janv, levels = c("C2", "C3", "C1"))? This at least should work in ggplot2 I feel like

[A-legac45]

It does not seem to work when I do

proj$cluster <- factor(proj$cluster,levels = c("c1", "c2", "c3"))

proj$cluster <- as.character(proj$cluster)

p1v <- plotGroups(
ArchRProj = proj,
groupBy = as.character("cluster"),
colorBy = "GeneExpressionMatrix",
name = c("Plac8", "Cldn10"),
plotAs = "violin",
alpha = 0.4,
addBoxPlot = TRUE,
log2Norm = TRUE,
imputeWeights = NULL
)

The order is not the expected on unfortunalty do you have another alternative?