R/PlotProteinTaxa.R

In Proteomicslab57357/UniprotR: Retrieving Information of Proteins from Uniprot

#' Connect and parse UniProt information.
#'
#' This Function is used to plot different taxas found of the accessions.
#'
#' @usage PlotProteinTaxa(ProteinDataObject , directorypath = NULL)
#'
#' @param ProteinDataObject input a Dataframe of proteins as rownames.
#'
#' @param directorypath path to save files returened by the function.
#'
#' @author Mohmed Soudy \email{Mohamed.soudy@57357.com} and Ali Mostafa \email{ali.mo.anwar@std.agr.cu.edu.eg}
#'
#' @export
#'
PlotProteinTaxa <- function(ProteinDataObject , directorypath = NULL)
{
  ChromoCount <- ddply(ProteinDataObject, .(ProteinDataObject$Organism), nrow)
  ChromoCount %>%
    mutate(freq = percent(ChromoCount$V1 / sum(ChromoCount$V1))) -> ChromoCount

  TaxaPlot <- ggplot(ChromoCount , aes(x = reorder(ChromoCount$`ProteinDataObject$Organism` , ChromoCount$V1) , y = ChromoCount$V1)) +
    geom_bar(aes(fill = ChromoCount$`ProteinDataObject$Organism`), stat = "identity" , alpha = 0.7) + ylab("Frequency") +guides(fill=guide_legend(title="Organisms"))+
    geom_text(aes(label = ChromoCount$freq), vjust = -0.3) + theme_bw() + theme(axis.text.x = element_text(angle = 45),axis.title.x  =  element_blank() , text = element_text(size=11, face="bold", colour="black"))
  plot(TaxaPlot)
  print(ChromoCount)
  if (!is.null(directorypath)){
    ggsave(paste0(directorypath, "//" ,"Proteins Taxonomy.jpeg") ,plot = TaxaPlot , device = "jpeg" , dpi = 320 , width =  10 , height = 8)
    ggsave(paste0(directorypath, "//" ,"Proteins Taxonomy.tiff") ,plot = TaxaPlot , device = "tiff" , dpi = 320 , width =  10 , height = 8)
  }
}