comparison topGO_enrichment.R @ 11:fa2e27165d5d draft

planemo upload commit 4efc56eb769fbceb66c64181441ff8781d523454-dirty

10:e3430084c996

  return(values)
}

createDotPlot = function(data, onto){
  
  values  = deleteInfChar(data$pvalues)
  values = roundValues(values)
  values = as.numeric(values)
  
  geneRatio = data$Significant/data$Annotated
  goTerms = data$Term
  count = data$Significant
  
  labely = paste("GO terms",onto,sep=" ")
  ggplot(data,aes(x=geneRatio,y=goTerms, color=values,size=count)) +geom_point( ) + scale_colour_gradientn(colours=c("red","violet","blue")) + xlab("Gene Ratio") + ylab(labely) + labs(color="p-values\n" ) 
  ggsave("dotplot.png", device = "png", dpi = 320, limitsize = TRUE, width = 15, height = 15, units="cm")
}

createBarPlot = function(data, onto){
  
  
  values  = deleteInfChar(data$pvalues)
  values = roundValues(values)
  values = as.numeric(values)
  
  goTerms = data$Term
  count = data$Significant
  
  labely = paste("GO terms",onto,sep=" ")
  ggplot(data, aes(x=goTerms, y=count,fill=values,scale(scale = 0.5))) + ylab("Gene count") + xlab(labely) +geom_bar(stat="identity") + scale_fill_gradientn(colours=c("red","violet","blue")) + coord_flip() + labs(fill="p-values\n") 
  ggsave("barplot.png", device = "png", dpi = 320, limitsize = TRUE, width = 15, height = 15, units="cm")
}

# Produce the different outputs
createOutputs = function(result, cut_result,text, barplot, dotplot, onto){
  
  if (is.null(result)){
    if (text){
      err_msg = "None of the input ids can be found in the org package data, enrichment analysis cannot be realized. \n The inputs ids probably either have no associated GO terms or are not ENSG identifiers (e.g : ENSG00000012048)."
      write.table(err_msg, file='result', quote=FALSE, sep='\t', col.names = T, row.names = F)
    }
    if (barplot){
      png(filename="barplot.png")
      plot.new()
      #text(0,0,err_msg)
      dev.off()
    }
    if (dotplot){
      png(filename="dotplot.png")
      plot.new()
      #text(0,0,err_msg)
      dev.off()
    }
    opt <- options(show.error.messages=FALSE)
    on.exit(options(opt))
    stop("null result")
  }
  
  if (is.null(cut_result)){
    if (text){
      err_msg = "Threshold was too stringent, no GO term found with pvalue equal or lesser than the threshold value."
      write.table(err_msg, file='result', quote=FALSE, sep='\t', col.names = T, row.names = F)
    }
    if (barplot){
      png(filename="barplot.png")
      plot.new()
      text(0,0,err_msg)
      dev.off()
    }
    if (dotplot){
      png(filename="dotplot.png")
      plot.new()
      text(0,0,err_msg)
      dev.off()
    }
    opt <- options(show.error.messages=FALSE)
    on.exit(options(opt))
    stop("null cut_result")
  }
  
  if (text){
    write.table(cut_result, file='result', quote=FALSE, sep='\t', col.names = T, row.names = F)
  }
  
  if (barplot){
    createBarPlot(cut_result, onto)
  }
  
  if (dotplot){
    createDotPlot(cut_result, onto)
  }
}

# Launch enrichment analysis and return result data from the analysis or the null
# object if the enrichment could not be done.

  sample = trimws(unlist(strsplit(tab[,column],";")))
}

#check of ENS ids
if (! any(check_ens_ids(sample))){
  print("no ensembl gene ids found in your ids list, please check your IDs in input or the selected column of your input file")
  stop()
}

#get input if background genes
if (background){
  if (background_input_type=="copy_paste"){

    background_tab=read_file(background_genes,background_header)
    background_sample = unique(trimws(unlist(strsplit(background_tab[,background_column],";"))))
  }
  #check of ENS ids
  if (! any(check_ens_ids(background_sample))){
    print("no ensembl gene ids found in your background ids list, please check your IDs in input or the selected column of your input file")
    stop()
  }
} else {
  background_sample=NULL
}

11:fa2e27165d5d

  return(values)
}

createDotPlot = function(data, onto){
  
    values  = deleteInfChar(data$pvalues)
    values = roundValues(values)
    values = as.numeric(values)
    
    geneRatio = data$Significant/data$Annotated
    goTerms = data$Term
    count = data$Significant
    
    labely = paste("GO terms",onto,sep=" ")
    ggplot(data,aes(x=geneRatio,y=goTerms, color=values,size=count)) +geom_point( ) + scale_colour_gradientn(colours=c("red","violet","blue")) + xlab("Gene Ratio") + ylab(labely) + labs(color="p-values\n" ) 
    ggsave("dotplot.png", device = "png", dpi = 320, limitsize = TRUE, width = 15, height = 15, units="cm")
}

createBarPlot = function(data, onto){
  
    values  = deleteInfChar(data$pvalues)
    values = roundValues(values)
    values = as.numeric(values)
    
    goTerms = data$Term
    count = data$Significant
    
    labely = paste("GO terms",onto,sep=" ")
    ggplot(data, aes(x=goTerms, y=count,fill=values,scale(scale = 0.5))) + ylab("Gene count") + xlab(labely) +geom_bar(stat="identity") + scale_fill_gradientn(colours=c("red","violet","blue")) + coord_flip() + labs(fill="p-values\n") 
    ggsave("barplot.png", device = "png", dpi = 320, limitsize = TRUE, width = 15, height = 15, units="cm")
}

# Produce the different outputs
createOutputs = function(result, cut_result,text, barplot, dotplot, onto){

  if (is.null(result)){
    err_msg = "None of the input ids can be found in the org package data, enrichment analysis cannot be realized. \n The inputs ids probably either have no associated GO terms or are not ENSG identifiers (e.g : ENSG00000012048)."
    write.table(err_msg, file='result', quote=FALSE, sep='\t', col.names = F, row.names = F)
  }else if (is.null(cut_result)){
    err_msg = "Threshold was too stringent, no GO term found with pvalue equal or lesser than the threshold value."
    write.table(err_msg, file='result.tsv', quote=FALSE, sep='\t', col.names = F, row.names = F)
  }else {
    write.table(cut_result, file='result.tsv', quote=FALSE, sep='\t', col.names = T, row.names = F)
  
    if (barplot){createBarPlot(cut_result, onto)}
    if (dotplot){createDotPlot(cut_result, onto)}
  }
}

# Launch enrichment analysis and return result data from the analysis or the null
# object if the enrichment could not be done.

  sample = trimws(unlist(strsplit(tab[,column],";")))
}

#check of ENS ids
if (! any(check_ens_ids(sample))){
  stop("no ensembl gene ids found in your ids list, please check your IDs in input or the selected column of your input file")
}

#get input if background genes
if (background){
  if (background_input_type=="copy_paste"){

    background_tab=read_file(background_genes,background_header)
    background_sample = unique(trimws(unlist(strsplit(background_tab[,background_column],";"))))
  }
  #check of ENS ids
  if (! any(check_ens_ids(background_sample))){
    stop("no ensembl gene ids found in your background ids list, please check your IDs in input or the selected column of your input file")
  }
} else {
  background_sample=NULL
}