Off topic:emapplot (enrichplot) with compareCluster object does not work
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Entering edit mode
4.2 years ago
rapmic • 0

Dear All

The sample from https://yulab-smu.github.io/clusterProfiler-book/chapter12.html results in the following:

> library(clusterProfiler)

> data(gcSample)

> xx <- compareCluster(gcSample, fun="enrichKEGG",
+                      organism="hsa", pvalueCutoff=0.05)

> p1 <- emapplot(xx)
Fehler in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'emapplot' for signature '"compareClusterResult"'

> p2 <- emapplot(xx,legend_n=2) 
Fehler in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'emapplot' for signature '"compareClusterResult"'

> p3 <- emapplot(xx,pie="count")
Fehler in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'emapplot' for signature '"compareClusterResult"'

> p4 <- emapplot(xx,pie="count", pie_scale=1.5, layout="kk")
Fehler in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'emapplot' for signature '"compareClusterResult"'

> cowplot::plot_grid(p1, p2, p3, p4, ncol=2, labels=LETTERS[1:4])
Fehler in cowplot::plot_grid(p1, p2, p3, p4, ncol = 2, labels = LETTERS[1:4]) : 
  Objekt 'p3' nicht gefunden

> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.2

Is there a solution for this problem?

Thank you in advance.

BW RM

emapplot enrichplot clusterProfiler compareCluster • 1.9k views
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