Problem retrieving graphics in clusterprofiler
3
0
Entering edit mode
@jose-luis-lavin-5531
Last seen 3.7 years ago
Spain

Dear All,

I'm experiencing a problem while using your super-useful packages DOSE and ClusterProfiler.
I try to create a for loop to process multiple genelists in batch. The script works generating the result-tables but fails to find the enrichment objects (namely ego's,ggo's, kk and kk2 that you'll see in the following script). It seems to me that they are unavailable after the table creation and can’t be found by the graphical functions (barplot, dotplot, enrichmap or cnetplot). If I run it out of the for loop, it works smoothly with a single list, I mean the exact same commands.

Here is the error I get when graphical functions (dotplot in this case) fail:

Error in dotplot(egoBP) :

error in evaluating the argument 'object' in selecting a method for function 'dotplot':

Error: object 'egoBP' not found


Here is my script in case you can tell me what can be the problem:


###############ClusterProfiler#############################

#install.packages(c("DOSE", "clusterProfiler"),repos="http://www.bioconductor.org/packages/devel/bioc")
# source("https://bioconductor.org/biocLite.R")
# biocLite (c("tidyr","pathview","Rgraphviz","RDAVIDWebService"))
#install.packages("rJava")
library(DOSE)
library(clusterProfiler)
#library(RDAVIDWebService)

x<-setwd("C:/R_data/Folder/")

file.list <- as.list(list.files(".", pattern = "*.tsv$"))
file.list

for(i in 1:length(file.list))
{
  #create the new output directory list
  dir<- gsub("\\.tsv$", "", file.list[[i]])
  file.path<-x
  dir.create(file.path(dir))
 
  #read the table
  geneList2<- read.table(file.list[[i]]) #For loop
  head(geneList2)
  str(geneList2)

  #generate vector
  gene.vector=geneList2$V2
  names(gene.vector)=geneList2$V1
  head(gene.vector)
 
  vlist<-gene.vector
  head(vlist)
  str(vlist)

  listaGenes <- as.vector(geneList2[,1])#
  head(listaGenes)
  genes<-as.character(listaGenes)#list of genes

  #Gene Ontology Classification Examples
  ggoBP <- groupGO(gene     = genes,
                   organism = "mouse",#organism = "human"
                   ont      = "BP",
                   level    = 3,
                   readable = TRUE)
  head(summary(ggoBP))
  write.csv(summary(ggoBP), file=(paste(file.path, dir,"GOc_GOBp_table.csv", sep="/")))
 
  #GO over-representation test
  egoBP <- enrichGO(gene          = genes,
                    universe      = allEntrez,
                    organism = "mouse",#organism = "human"
                    ont           = "BP",
                    pAdjustMethod = "BH",
                    pvalueCutoff  = 0.1,#pvalueCutoff  = 0.01,
                    qvalueCutoff  = 0.05,
                    readable      = TRUE)
  head(summary(egoBP))
  write.csv(summary(egoBP), file=(paste(file.path, dir,"Overrep_GOBP_table.csv", sep="/")))
 
  #GO Gene Set Enrichment Analysis
  ego2BP <- gseGO(geneList     = vlist,
                  organism = "mouse",#organism = "human"
                  ont          = "BP",
                  nPerm        = 1000,
                  minGSSize    = 5,#120,
                  pvalueCutoff = 0.5,#pvalueCutoff = 0.01,
                  verbose      = FALSE)
  write.csv(summary(ego2BP), file=(paste(file.path, dir,"gseGOBP_table.csv", sep="/")))
 
  #KEGG over-representation test
  kk <- enrichKEGG(gene         = genes,
                   organism     = "mouse",#organism     = "human",
                   pvalueCutoff = 0.05,
                   readable     = TRUE)
  #use_internal_data = TRUE)
  head(summary(kk))
  write.csv(summary(kk), file=(paste(file.path, dir,"enrichKEGG_table.csv", sep="/")))
 
  #Graphical Visualization Examples
  #Barplot
  pdf(paste(file.path, dir, "Enrichment_barplot.pdf", sep="/"))
  barplot(egoBP, showCategory=8,font.size=5)
  dev.off()

  #Dotplot
   pdf(paste(file.path, dir, "Enrichment_dotplot.pdf", sep="/"))
  dotplot(egoBP)
  dev.off()
 
  #Enrichmap
   pdf(paste(file.path, dir, "Enrichment2_Map.pdf", sep="/"))

  enrichMap(egoBP,vertex.label.cex=1.2,layout=igraph::layout.kamada.kawai)
  dev.off()
 
  #cnetplot
  pdf(paste(file.path, dir, "Enrichment_Cnet.pdf", sep="/"))
  cnetplot(egoBP, categorySize="pvalue", foldChange=vlist)
  dev.off()
 
  #Networks
  pdf(paste(file.path, dir, "Enrichment_Networks.pdf", sep="/"))
  plotGOgraph(egoBP)
  dev.off()
}


 

> sessionInfo()

R version 3.2.2 (2015-08-14)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows 7 x64 (build 7601) Service Pack 1

 

locale:

[1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252  

[3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C                 

[5] LC_TIME=Spanish_Spain.1252   

 

attached base packages:

 [1] grid      parallel  stats4    stats     graphics  grDevices utils   

 [8] datasets  methods   base    

 

other attached packages:

 [1] pathview_1.10.1       org.Hs.eg.db_3.2.3    Rgraphviz_2.14.0    

 [4] graph_1.48.0          SparseM_1.7           GO.db_3.2.2         

 [7] org.Mm.eg.db_3.2.3    AnnotationDbi_1.32.0  IRanges_2.4.4       

[10] S4Vectors_0.8.3       Biobase_2.30.0        BiocGenerics_0.16.1 

[13] clusterProfiler_2.4.3 DOSE_2.8.3            RSQLite_1.0.0       

[16] DBI_0.3.1           

 

loaded via a namespace (and not attached):

 [1] Rcpp_0.12.2       plyr_1.8.3        XVector_0.10.0    tools_3.2.2     

 [5] zlibbioc_1.16.0   digest_0.6.8      lattice_0.20-33   gtable_0.1.2    

 [9] png_0.1-7         KEGGgraph_1.28.0  igraph_1.0.1      curl_0.9.4      

[13] proto_0.3-10      topGO_2.22.0      stringr_1.0.0     httr_1.0.0      

[17] Biostrings_2.38.2 qvalue_2.2.2      R6_2.1.1          XML_3.98-1.3    

[21] GOSemSim_1.28.2   ggplot2_1.0.1     reshape2_1.4.1    DO.db_2.9       

[25] magrittr_1.5      scales_0.3.0      MASS_7.3-45       splines_3.2.2   

[29] KEGGREST_1.10.1   colorspace_1.2-6  labeling_0.3      stringi_1.0-1   

[33] munsell_0.4.2

 

software error clusterprofiler GO genesetenrichment • 1.9k views
ADD COMMENT
1
Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months ago
China/Guangzhou/Southern Medical Univer…

 

I can't reproduce your issue.

Although you should explicitly call print(dotplot()) since the function return ggplot object, it won't complain object not found if it is exists.

 

 

ADD COMMENT
0
Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months ago
China/Guangzhou/Southern Medical Univer…

Error in dotplot(egoBP) :

error in evaluating the argument 'object' in selecting a method for function 'dotplot':

Error: object 'egoBP' not found

 

object not found! this is explictly.

 

for(i in 1:length(file.list))
{

print(i)

 

...

}

 

Maybe you can print i before processing the file to help identifying which file have the issue.

 

ADD COMMENT
0
Entering edit mode
Dear Guangchuang Yu,

I did that in a previous version of the code, and I did confirm my lists entered the loop (In fact, as I said before, lists are processed and the different csv tables are retrieved. The problem comes when the plotting functions try to find the objects such as "egoBP".

Is at that point when the object can't be found, but ironically It was found previously for this process, e.g.:

write.csv(summary(egoBP), file=(paste(file.path, dir,"Overrep_GOBP_table.csv", sep="/")))

If the object is present to print its summary into a csv, how can it dissapear when I call the dotplot function inside the same loop a few lines after? e.g.

#Dotplot
   pdf(paste(file.path, dir, "Enrichment_dotplot.pdf", sep="/"))
  dotplot(egoBP)
  dev.off()

 

I suspect that it could be related with R language itself, not only to clusterProfile package specifically, that is why I published such a big piece of code...due to this I decided to post this issue to the list, just in case I have made a newbie mistake I am unable to detect.

Anyway, as I told you before, out of the "For loop" you code works perfectly well.

Thanks in advance for your attention.

JL

ADD REPLY
0
Entering edit mode
@jose-luis-lavin-5531
Last seen 3.7 years ago
Spain

Thank you Guangchuang Yu!

Explicitly calling print(dotplot()) and print(barplot()), did the trick and allowed me to obtain the graphics inside the FOR loop.

Thank you also for this remarkable package

Best wishes

 

JL

 

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