clusterProfiler setup specified order
1
0
Entering edit mode
joseph ▴ 50
@joseph-5658
Last seen 7.1 years ago

I have time-course data as "Day1", "Day2"....., when I create the list for compareCluster(), I have named the order as levels(list) = c("Day1","Day2"....), and I check the compareCluster() result, CompGO@compareClusterResult$Cluster, shows the order is "Day1", "Day2".... However, when I plot the data, the X-axis show the disorder characters. How can I fix the problem?
clusterProfiler • 3.2k views
ADD COMMENT •
0
Entering edit mode

show me the code

ADD REPLY •
0
Entering edit mode

list = list(Day1 = Day1, Day2 = Day2, Day3 = Day3......)

levels(list) = c("Day1","Day2","Day3"....)

lx = compareCluster(list)

dotplot(lx)

ADD REPLY •
0
Entering edit mode

already fixed, <https://github.com/GuangchuangYu/clusterProfiler/commit/7fda4a36409a112c5b994dbbef47483aa3929f9a>.

The order in input list will be maintained when plotting.

ADD REPLY •
0
Entering edit mode

should I update to the latest version? I install the ver-3.4.1. The one you fixed in your developed version?

BTW, after compareCluster(), might be some time point not have the gene clusters, but in order to present the time-course data, can I keep show up all time points data, even if some of them haven't significant enriched pathway/GO? 

ADD REPLY •
0
Entering edit mode

Could you please clarify how to place the specific order on the x-axis? And keep some groups even they don't have enriched result, just to show the longitudinal data,  

ADD REPLY •
0
Entering edit mode
joseph ▴ 50
@joseph-5658
Last seen 7.1 years ago

And one more problem when I use enricher() function, also return no gene mapped:

egmt_go <- enricher(DEG_Day9_ENTREZID, TERM2GENE = c_go,
+                     pvalueCutoff = 0.5, pAdjustMethod = "BH", universe,
+                     minGSSize = 10, maxGSSize = 500, qvalueCutoff = 0.2)
--> No gene can be mapped....
--> Expected input gene ID: DNAJB1,ZFP36,PDE3A,POLE,AADAT,DIS3
--> return NULL...

 

The genes have been converted into EntrezID, more than 500 gene, should be match to GO or KEGG database.
ADD COMMENT •
0
Entering edit mode

your c_go contains gene symbol while DEG_Day9_ENTREZID is entrezgene ID.

​
ADD REPLY •
0
Entering edit mode

I use entrezID for both of them, but has the error as

> egmt_kegg <- enricher(DEG_Day9_ENTREZID, TERM2GENE = c_kegg,
+                       pvalueCutoff = 0.1, pAdjustMethod = "BH", universe,
+                       minGSSize = 10, maxGSSize = 500, qvalueCutoff = 0.2)
Error in as.vector(x, mode) :
  cannot coerce type 'closure' to vector of type 'any'

ADD REPLY •
0
Entering edit mode

you need to provide a reproducible example as described in <http://guangchuangyu.github.io/2016/07/how-to-bug-author/>.

 

ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 565 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6