Comments (4)
huerqiang
commented on June 11, 2024
1
@guidohooiveld Will be fixed in #260
test_treeplot.pdf
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guidohooiveld
commented on June 11, 2024
You did not show your full code, but if you create the input list for the function compareCluster using the order you would like to, these order is retained in the resulting treeplot.
Admittedly, the resulting plot is not nice; ideally the labels should be rotated 90 degrees, and also the dots are positioned outside the colored clusterPanel...
@huerqiang : could you please have a look at these 2 issues (option to rotate labels, and correct position dots)?
Thanks!
> ## load libraries
> library(clusterProfiler)
> library(enrichplot)
> library(org.Hs.eg.db)
> library(ggplot2)
>
> ## load sample data
> data(gcSample)
>
> ## keep first 5 samples
> gcSample1 <- gcSample[c(1:5)]
>
> ## rename first 5 samples
> ## use increasing order
> names(gcSample1)[1:5] <- c("12", "146", "682", "1450", "1960")
>
> ## run enrichGO
> data.out.bp1 <- compareCluster(gcSample1, fun="enrichGO",
+ OrgDb="org.Hs.eg.db", ont="BP", pvalueCutoff=0.05)
>
> data.out.bp1 <- pairwise_termsim(data.out.bp1)
>
>
> ## make treeplot
> ## note: changed showCategory to 3
>
>
> p1 <- treeplot(data.out.bp1,showCategory=3,
+ clusterPanel.params = list(clusterPanel = "dotplot") )
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
ℹ invalid tbl_tree object. Missing column: parent,node.
ℹ invalid tbl_tree object. Missing column: parent,node.
>
> ## show picture
> p1
>
> ## rename samples, but now use random order
> gcSample2 <- gcSample[c(1:5)]
> names(gcSample2)[1:5] <- c("146", "12", "682", "1960", "1450")
>
> ## run enrichGO again
> data.out.bp2 <- compareCluster(gcSample2, fun="enrichGO",
+ OrgDb="org.Hs.eg.db", ont="BP", pvalueCutoff=0.05)
>
> data.out.bp2 <- pairwise_termsim(data.out.bp2)
>
> p2 <- treeplot(data.out.bp2,showCategory=3,
+ clusterPanel.params = list(clusterPanel = "dotplot") )
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
ℹ invalid tbl_tree object. Missing column: parent,node.
ℹ invalid tbl_tree object. Missing column: parent,node.
>
> ## show picture
> p2
>
>
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huerqiang
commented on June 11, 2024
@guidohooiveld It will be fixed in a few days.
from enrichplot.
guidohooiveld
commented on June 11, 2024
@huerqiang : thanks for implementing a fix for this so quickly! Much appreciated.
from enrichplot.
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