cluster profiler visualization

Question

[neo.wongcilik]

Dear everybody, I do need help I'm a beginner in R Bioconductor, now i'm try to visualizing my data which I got from DAVID analysis to get the cluster gene and bar blot, however i'm stuck on it. Here, i'm attached my problem, help me please, and thank you.

>library(readr)
> Funct_Annot_Clust <- read_csv("/Users/Ahmad Suparmin/OneDrive - Shizuoka University/Transcriptome 2017/all sample/RESULT/DifferentialExpression/David Analysis/Test 8/Up/Funct Annot Clust.txt")
Parsed with column specification:
cols(
  `Annotation Cluster 1 Enrichment Score: 5.3164343530168` = col_character()
)
Warning: 172 parsing failures.
row # A tibble: 5 x 5 col     row col   expected  actual      file                                                                                          expected   <int> <chr> <chr>     <chr>       <chr>                                                                                         actual 1     2 NA    1 columns 219 columns '/Users/Ahmad Suparmin/OneDrive - Shizuoka University/Transcriptome 2017/all sample/RESULT/D~ file 2     3 NA    1 columns 223 columns '/Users/Ahmad Suparmin/OneDrive - Shizuoka University/Transcriptome 2017/all sample/RESULT/D~ row 3     4 NA    1 columns 218 columns '/Users/Ahmad Suparmin/OneDrive - Shizuoka University/Transcriptome 2017/all sample/RESULT/D~ col 4     5 NA    1 columns 218  [... truncated]
Warning message:
In rbind(names(probs), probs_f) :
  number of columns of result is not a multiple of vector length (arg 1)
> View(Funct_Annot_Clust)
> FD<-Funct_Annot_Clust
> FD
# A tibble: 249 x 1
   `Annotation Cluster 1\tEnrichment Score: 5.3164343530168`                                                                
   <chr>                                                                                                                    
 1 "Category\tTerm\tCount\t%\tPValue\tGenes\tList Total\tPop Hits\tPop Total\tFold Enrichment\tBonferroni\tBenjamini\tFDR"  
 2 "GOTERM_CC_DIRECT\tGO:0016021~integral component of membrane\t219\t22.577319587628867\t1.5869101931958633E-14\tCCM_07104"
 3 "UP_KEYWORDS\tMembrane\t223\t22.989690721649485\t0.0026452898978343914\tCCM_06620"                                       
 4 "UP_KEYWORDS\tTransmembrane helix\t218\t22.474226804123713\t0.0035248991883832194\tCCM_07104"                            
 5 "UP_KEYWORDS\tTransmembrane\t218\t22.474226804123713\t0.003665137431804559\tCCM_07104"                                   
 6 "Annotation Cluster 2\tEnrichment Score: 4.8192542759257"                                                                
 7 "Category\tTerm\tCount\t%\tPValue\tGenes\tList Total\tPop Hits\tPop Total\tFold Enrichment\tBonferroni\tBenjamini\tFDR"  
 8 "INTERPRO\tIPR020846:Major facilitator superfamily domain\t51\t5.257731958762887\t3.608857555807972E-6\tCCM_06620"       
 9 "GOTERM_BP_DIRECT\tGO:0055085~transmembrane transport\t40\t4.123711340206185\t2.272734359010133E-5\tCCM_06089"           
10 "INTERPRO\tIPR011701:Major facilitator superfamily\t36\t3.711340206185567\t4.2493133146939425E-5\tCCM_06089"             
# ... with 239 more rows
> FD <- enricher(gene, TERM2GENE=MF)
Error in as.data.frame(path2gene) : object 'MF' not found
> FD <- enricher(gene, TERM2GENE=FD)
Error in path2gene[, 2] : incorrect number of dimensions
> FD <- enricher(gene, TERMGENE=FD)
Error in enricher(gene, TERMGENE = FD) : unused argument (TERMGENE = FD)
> FD <- enricher(gene, TERM2GENE=FD)
Error in path2gene[, 2] : incorrect number of dimensions
> FD2 <- GSEA(geneList, TERM2GENE=FD, verbose=FALSE)
Error in path2gene[, 2] : incorrect number of dimensions
> head(FD2)
Error in head(FD2) : object 'FD2' not found
> barplot(ggo, drop=TRUE, showCategory=12)
> FD <- enricher(gene, GOTERM_MF_DIRECT)
Error in build_Anno(TERM2GENE, TERM2NAME) : 
  argument "TERM2GENE" is missing, with no default
> FD <- enricher(gene, TERM2GENE=GOTERM_MF_DIRECT)
Error in as.data.frame(path2gene) : object 'GOTERM_MF_DIRECT' not found

[Ram]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Answer 1

[Kevin Blighe]

Your major error is from your very first step. You are reading your file as comma-separated values (CSV) file; however, it is clearly a tab-separated values (TSV) file.

Try this, instead:

Funct_Annot_Clust <- read.table("/Users/Ahmad Suparmin/OneDrive - Shizuoka University/Transcriptome 2017/all sample/RESULT/DifferentialExpression/David Analysis/Test 8/Up/Funct Annot Clust.txt", sep="\t", stringsAsFactors=FALSE, header=TRUE)

You will also help yourself a lot in the future by not using spaces in your filenames (including directories). Also try to minimise the use of other punctuation. Just use alpha-numeric characters.

Kevin