R/motif_from_clusterfile.R

In ClusTCR2: Identifying Similar T Cell Receptor Hyper-Variable Sequences with 'ClusTCR2'

#' Code for plotting the Motif based on a specific CDR3 length and V gene (see [netplot_ClusTCR2] for details).
#' @param ClusTCR Cluster file produced from [mcl_cluster].
#' @param Clust_selected Select which cluster to review.
#' @param selected_cluster_column Select the column "Clust_size_order" of the cluster ordered.
#' @return A ggplot object representing the motif.
#' @importFrom  VLF aa.count.function
#' @importFrom ggseqlogo ggseqlogo
#' @import ggplot2
#' @export

Motif_from_cluster_file <- function(ClusTCR, Clust_selected=NULL,selected_cluster_column = "Clust_size_order") {
  source(system.file("Functions","motifStack.functions.R",package = "ClusTCR2"))
  motif_DF <- ClusTCR
  z1 <- as.data.frame(t(as.data.frame(strsplit(motif_DF$CDR3_Vgene,"_"))))
  motif_DF$motif <- z1$V1

  motif_DF$len1 <- nchar(motif_DF[,names(motif_DF) %in% "motif"])
  motif_DF$Clust_size_order2 <- motif_DF[,names(motif_DF) %in% selected_cluster_column]

  if (length(which(motif_DF$Clust_size_order2==c(Clust_selected)))>0) {
    motif_DF_interest <- motif_DF[motif_DF$Clust_size_order2 %in% c(Clust_selected),]
    # subset(motif_DF,motif_DF$cluster==Clust_selected)
    motif <- as.data.frame(t(as.data.frame(strsplit(motif_DF_interest$motif, ""))))
    len <- nchar(unique(motif_DF_interest$motif))[1]
    motif_count <- aa.count.function(cbind(x=1,y=2,motif),len)
    motif_count1_aa<-pcm2pfm(motif_count)
    ggseqlogo(motif_count, seq_type='aa', method='p') +
      ylab('bits')+
      geom_hline(yintercept=0) +
      geom_vline(xintercept=0) +
      theme(
        axis.text.x = element_text(colour="black",size=20,angle=0,hjust=.5,vjust=.5,face="plain",family="serif"),
        axis.text.y = element_text(colour="black",size=20,angle=0,hjust=1,vjust=0,face="plain",family="serif"),
        axis.title.x=element_text(colour="black",size=20,angle=0,hjust=.5,vjust=.5,face="plain",family="serif"),
        axis.title.y = element_text(colour="black",size=20,angle=90,hjust=.5,vjust=.5,face="plain",family="serif"),
        legend.title  =element_blank(),
        legend.position = "right",
        legend.text = element_text(colour="black", size=12,family="serif")
      )

  }

  else {
    paste0("Cluster, ", Clust_selected,", does not exist")

  }
}