Describe the bug I am trying to create bar plots of my ORA result

Hi, this issue is due to the duplicated terms in test_ego. <div class="snippet-cli

ORA result plotting error because of duplicated terms about genekitr HOT 1 CLOSED

ganglilab commented on June 9, 2024

ORA result plotting error because of duplicated terms

from genekitr.

Comments (1)

reedliu commented on June 9, 2024

Hi, this issue is due to the duplicated terms in test_ego.

library(genekitr)
library(geneset)
library(dplyr)
gs3 <- getReactome(org = "human")
testgenes <- read.csv(file = "~/Downloads/for_R_test/testgenelist.csv", header = TRUE, sep = ",")
## ORA Analysis
id <- testgenes$GeneID
test_ego <- genORA(id,
                   geneset = gs3,
                   p_cutoff = 0.05,
                   q_cutoff = 0.10
)

# check duplicated term
description <- test_ego$Description
dup_term <- description[duplicated(description)] # "Maturation of nucleoprotein"

# get IDs
dup_term_ids <- test_ego %>% filter(Description == dup_term) %>% pull(ID)
# "R-HSA-9683610" "R-HSA-9694631"

You can see both R-HSA-9694631 and R-HSA-9683610 all belong to "Maturation of nucleoprotein". While the Y-axis of the plot does not support duplicated terms.

So the solution is to make the duplicated terms unique.
For example, we could combine Reactome IDs with "Maturation of nucleoprotein".

# modify duplicated description
test_ego <- test_ego %>% mutate(Description = if_else(Description %in% dup_term,
                                          paste0(Description,'_',ID),
                                          Description))
plotEnrich(test_ego, plot_type = "bar")