pointSize, labSize, and DrawConnectors error when plotting EnhancedVolcano
I just re-downloaded Rstudio (v1.3) and EnhancedVolcano from:
if (!requireNamespace('BiocManager', quietly = TRUE))
install.packages('BiocManager')
BiocManager::install('EnhancedVolcano')
pointSize, labSize, are not autocompleting when typing the condition in my EnhancedVolcano script, which leads me to believe it is not recognized in my package.
DrawConnectors autocompletes, but when used does not generate a plot (plot window in Rstudio is completely blank).
If I do not include DrawConnectors, pointSize, or labSize, the plot generates, but when included I lose the plot
Error in EnhancedVolcano(df1, lab = row.names(df1), x = "log2FC", y = "Age.Adjusted.FDR", :
unused arguments (pointSize = c(ifelse(df1$log2FC > 0.3, 8, 1)), drawConnectors = TRUE)
EnhancedVolcano(df1,
lab = row.names(df1),
x = "log2FC",
y = "Age.Adjusted.FDR",
ylab = bquote(~-Log[10]~italic(FDR)),
title = "Volcano Plot",
pCutoff = 0.2,
FCcutoff = 0.3,
legendPosition = "right",
pointSize = c(ifelse(df1$log2FC > 0.3, 8, 1)),
labSize = 4.0,
col=c("black", "orange", "blue", "red"),
legend=c("NS","Log2 FC > |0.3|","FDR < 0.2","FDR < 0.2 & Log2 FC > |0.3|"),
drawConnectors = TRUE,
ylim = c(0,-log10(10e-4))
)
Is there an obvious reason I'm missing as to why these lines aren't working? Or an alternative method to increase the point size and label size of specific genes?
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Hello holmkn!
The EnhancedVolcano developer prefers that questions on the software be posted on the bioconductor support site.
Please post on https://support.bioconductor.org/
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Cheers!