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Emmaplot with the top activated and supressed from dotplot? #658
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If you would like to show in the
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Thank you very much for your response, and sorry for not explaining this issue in more detail: , and the scripts I've been using: library(clusterProfiler) g2 = clusterProfiler::dotplot(gse, showCategory=10, split=".sign") + facet_grid(.~.sign) matched_indices = p1@result$Description[p1@result$Description %in% terms] checked the order of terms for terms and matched_indicesenrichplot::emapplot(p1 , showCategory= matched_indices) Error in pair_sim[as.character(enrichDf$Description), as.character(enrichDf$Description)] :subscript out of boundsThanks in advance! |
When posting, please format your code! Select that text, and use the I could reproduce your problem with the provided
Note that the total number of significant gene sets in your object
.... whereas the dimensions of the similarity matrix is (only) 200 x 200:
This is because for the function Combine this with fact that within It thus turns out that some of gene sets that have a large This can be simply solved by calculating the similarity matrix for all gene sets, and not only the top 200. Therefore (note that I also modified [the order of] your code slightly):
dotplot g2: |
That worked perfectly! |
Hello dear Clusterprofiler team!
When segregating for activated and suppressed terms (dotplot with sign split), I want to make an emmaplot with the same top 20 terms from the dotplot. Is that possible? Thank you very much in advance
library(DOSE)
library(clusterProfiler)
library(enrichplot)
data(geneList)
edo2 <- gseDO(geneList)
clusterProfiler::dotplot(edo2, showCategory=10, split=".sign") + facet_grid(.~.sign)
edo <- pairwise_termsim(edo2)
emapplot(edo, showCategory=20) ## This will take the first terms, based on pvalues, and I want to plot the top 10 activated and top 10 suppressed from the dotplot.
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