plotExprs warning message: The dot-dot notation (`..ndensity..`) was deprecated in ggplot2 3.4.0.

[AHearn46]

Hi.

I recieved the error below when running my code. Iddly I ran the exact same code on the same dataset yesterday and all was well. I am new to R so sorry if this is basic but I can't work out how to fix it.

Thanks!

Error:

Warning message: The dot-dot notation (..ndensity..) was deprecated in ggplot2 3.4.0. ℹ Please use after_stat(ndensity) instead. ℹ The deprecated feature was likely used in the CATALYST package. Please report the issue at https://github.com/HelenaLC/CATALYST/issues.

Code:

directory<- setwd("/Users/k2030328/Library/CloudStorage/OneDrive-King'sCollegeLondon/SHAMAL/CyTOF Files/sub pops/blood/T")
md <- "T Cell_metadata.xlsx"

md <- read_excel(md)
class(md)
head(data.frame(md))
panel <- "WB_panel_V2.xlsx"
panel <-read_excel(panel)
fs<- read.flowSet(pattern = ".fcs", path = ".")
# spot check that all panel columns are in the flowSet object
all(panel$fcs_colname %in% colnames(fs)) 

#check which columns dont match
panel$fcs_colname[!panel$fcs_colname %in% colnames(fs)]

# specify levels for conditions & sample IDs to assure desired ordering
md$condition <- factor(md$condition, levels = c("Pre_Wean", "Post_Wean","Pre_Control","Post_Control"))
md$sample_id <- factor(md$sample_id, 
                       levels = md$sample_id[order(md$condition)])

str(md)
str(md$condition)

# construct SingleCellExperiment

sce <- prepData(fs, panel, md, features = panel$fcs_colname)

p <- plotExprs(sce, color_by = "condition")
p$facet$params$ncol <- 6
p 

[HelenaLC]

Should be fixed.