Question: (Closed) emapplot (enrichplot) with compareCluster object does not work
0
gravatar for rapmic
10 weeks ago by
rapmic0
rapmic0 wrote:

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

ADD COMMENTlink written 10 weeks ago by rapmic0

I see that you've asked this on the right forum: https://support.bioconductor.org/

Please do not cross-post. I'm closing this as it is more suited for bioconductor forum.

ADD REPLYlink written 10 weeks ago by RamRS26k

Hello rapmic!

We believe that this post does not fit the main topic of this site.

OP has cross-posted to bioC forum, where it belongs.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 10 weeks ago by RamRS26k
Please log in to add an answer.
The thread is closed. No new answers may be added.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1052 users visited in the last hour