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Question: clusterProfiler setup specified order
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gravatar for joseph
6 months ago by
joseph40
joseph40 wrote:

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?

ADD COMMENTlink modified 6 months ago • written 6 months ago by joseph40

show me the code

ADD REPLYlink written 6 months ago by Guangchuang Yu800

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

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

lx = compareCluster(list)

dotplot(lx)

ADD REPLYlink written 6 months ago by joseph40

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

The order in input list will be maintained when plotting.

ADD REPLYlink written 6 months ago by Guangchuang Yu800

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 REPLYlink written 6 months ago by joseph40

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 REPLYlink written 6 months ago by joseph40
0
gravatar for joseph
6 months ago by
joseph40
joseph40 wrote:

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 COMMENTlink written 6 months ago by joseph40

your c_go contains gene symbol while DEG_Day9_ENTREZID is entrezgene ID.

ADD REPLYlink written 6 months ago by Guangchuang Yu800

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 REPLYlink written 6 months ago by joseph40

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

 

ADD REPLYlink written 6 months ago by Guangchuang Yu800
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