GOSt Plot

I have been using GOSt in R to run GO analysis and create a plot with various terms highlighted. All went well, data exported etc but as someone relatively unfamiliar with R I have two questions.

How do I change the point size on the plot? I know how to do this in ggplot, but can't find a command here to do this, even though the cran package says this is now a ggplot object.
Can I export a plot from R as a PDF (so it would be a vector object in publishing software)? I can only find the options fro jpeg or png.

Thank you! For reference, here is my script:

install.packages("gprofiler2")
library(gprofiler2)

input <- as.vector(Genes_DMR_Stage[,'Gene'])

gostres <- gost(query = input, 
                organism = "hsapiens", ordered_query = FALSE, 
                multi_query = FALSE, significant = TRUE, exclude_iea = FALSE, 
                measure_underrepresentation = FALSE, evcodes = FALSE, 
                user_threshold = 0.05, correction_method = "fdr", 
                domain_scope = "annotated", custom_bg = NULL, 
                numeric_ns = "", sources = NULL, as_short_link = FALSE, highlight = TRUE)

df <- as.data.frame(gostres$result)
df <- apply(da,2,as.character)
write.csv2(df, "GO.csv")

p <- gostplot(gostres, capped = FALSE, interactive = FALSE)

pp <- publish_gostplot(p, highlight_terms = c("GO:0032502", "GO:0048856", "GO:0048869", "GO:0051216", "GO:0060173", "GO:0001501"), 
                       width = NA, height = NA, filename = NULL)

gost ggplot2

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updated 2.9 years ago by bk11 •

• written 2.9 years ago by Sarah •

2 answers

A hacky solution would be to use trace(gostplot, edit=TRUE) and manually change the size of the points. Changes are temporary and not reproducible. You could also recreate the Manhattan plot in ggplot so you have more control over it.

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written 2.9 years ago by Trivas •

How do I change the point size on the plot? I know how to do this in ggplot, but can't find a command here to do this, even though the cran package says this is now a ggplot object.

You can use ggplot function scale_size_continuous(range = c(x,y)) to increase or decrease the point sizes.

p <- gostplot(gostres, capped = TRUE, interactive = FALSE)+scale_size_continuous(range = c(5,10))

Can I export a plot from R as a PDF (so it would be a vector object in publishing software)? I can only find the options fro jpeg or png.

You can save your plot as pdf.

pdf("publish_gostplot.pdf", h=6, w=8)
pp <- publish_gostplot(p, highlight_terms = c("GO:0032502", "GO:0048856", "GO:0048869", "GO:0051216", "GO:0060173", "GO:0001501"), 
                       width = NA, height = NA, filename = NULL)
dev.off()

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written 2.9 years ago by bk11 •