Question: clusterProfiler - how does showCategory work in dotplot from compareClusterResult class?
0
gravatar for Jane Merlevede
3.1 years ago by
Jane Merlevede90 wrote:

Dear all,

I am using dotplot() to visualize results from enrichGO(), enrichDO(), enricher() and compareCluster() in clusterProfiler R package. When specifying showCategory, I get the right number of categories except with the results of compareCluser().

In my case, I use compareCluster() on a list of 3 elements:

 

str(ClusterList)
List of 3
 $ All : chr [1:1450] "89886" "29923" "100132891" "101410536" ...
 $ g1  : chr [1:858] "89886" "29923" "100132891" "101410536" ...
 $ g2: chr [1:592] "5325" "170691" "29953" "283392" ...
CompareGO_BP=compareCluster(ClusterList, fun="enrichGO", pvalueCutoff=0.01, pAdjustMethod="BH", OrgDb=org.Hs.eg.db,ont="BP",readable=T)

dotplot(CompareGO_BP, showCategory=10, title="GO - Biological Process")

 

I ask for 10 categories, but I get 15 categories in All, 8 categories in g1 and 12 categories in g2. None of the categories, neither the sum of the categories are 10...

Is the option showCategory working in the case of comparison? Am I missing something here?

And which categories precisely will it plot? the most significant whatever my 3 cases or the most significant of each case?

 

sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=fr_FR.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] clusterProfiler_3.2.1 DOSE_3.0.1           

loaded via a namespace (and not attached):
 [1] igraph_1.0.1         Rcpp_0.12.7          AnnotationDbi_1.36.0 magrittr_1.5         splines_3.3.1        BiocGenerics_0.20.0  IRanges_2.8.0        munsell_0.4.2       
 [9] BiocParallel_1.8.0   colorspace_1.2-6     fastmatch_1.0-4      stringr_1.0.0        plyr_1.8.4           tools_3.3.1          parallel_3.3.1       grid_3.3.1          
[17] Biobase_2.34.0       data.table_1.9.6     gtable_0.1.2         DBI_0.5-1            assertthat_0.1       tibble_1.2           GOSemSim_2.0.0       gridExtra_2.2.1     
[25] tidyr_0.6.0          reshape2_1.4.2       DO.db_2.9            ggplot2_2.1.0        S4Vectors_0.12.0     qvalue_2.6.0         RSQLite_1.0.0        stringi_0.5-5       
[33] fgsea_1.0.0          GO.db_3.4.0          scales_0.4.0         stats4_3.3.1         chron_2.3-47       

 

Thank you in advance for your help,

Jane

clusterprofiler • 1.4k views
ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Jane Merlevede90
Answer: clusterProfiler - how does showCategory work in dotplot from compareClusterResul
0
gravatar for Guangchuang Yu
3.1 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

see my answer in http://guangchuangyu.github.io/2016/11/showcategory-parameter-for-visualizing-comparecluster-output/

ADD COMMENTlink written 3.1 years ago by Guangchuang Yu1.1k

I think it would be better to also post here an answer, or at least an explanation, otherwise is difficult to know the answer if you change your username on github for example.

ADD REPLYlink written 3.1 years ago by Lluís Revilla Sancho530
Answer: clusterProfiler - how does showCategory work in dotplot from compareClusterResul
0
gravatar for Jane Merlevede
3.1 years ago by
Jane Merlevede90 wrote:

Thank you for the clarification

ADD COMMENTlink written 3.1 years ago by Jane Merlevede90
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