insert plot inside RStudio chunk fails

[splaisan]

Hi,

I tried this code in a Rscript and it works When used in a Rmd chunk, it does not and returns No plot to insert.NULL although the plot is shown below the chunk block after the print(p0) command (the plot is not added to the plot pane which is I think the reason for the fail)

Can I make this to work in RStudio in a Rmd file?

Thanks

p0a <- ggplot(read.data, aes(y=read, x=sampleID)) + 
  geom_bar(position="stack", stat="identity") +
  coord_flip() +
  theme(axis.text.y=element_text(size=rel(0.75))) +
  ggtitle("Demultiplexed read pair counts")

p0b <- ggplot(read.data, aes(y=read)) + 
  geom_boxplot(outlier.colour="black", outlier.shape=16, outlier.size=2, notch=TRUE) +
  theme(axis.title.y=element_blank(), axis.title.x=element_blank(), axis.text.x=element_blank(), axis.ticks.x=element_blank())

p0 <- ggarrange(p0a, p0b, nrow = 1, widths = c(6,1))

# add to excel file
wb <- createWorkbook()

# add worksheets
addWorksheet(wb, "read_count")
writeData(wb, "read_count", read.data[, c('sampleID', 'read')], startCol = 1, startRow = 1, rowNames = FALSE)
print(p0)
insertPlot(wb, "read_count", xy = c("D", 2), width = 5, height = 3.5, fileType = "png", units = "in")

addWorksheet(wb, "chain_count")
addWorksheet(wb, "clonotype_count", tabColour = "red")

saveWorkbook(wb, file = "runQC/results.xlsx", overwrite = TRUE)

[splaisan]

found a fix, changing the way plots are inserted as described in https://community.rstudio.com/t/plots-not-showing-up-in-the-plots-pane-in-rstudio/3981/5 did it