R/plotSNE.R

In douve/viRievac: Main R functions (viRievac)

# tSNE plot
plotSNE = function(data,vars=c('tSNE_V1','tSNE_V2'), col.clusters =F,
                   clusters.var='louvain',palette=NULL,label=F,
                   alpha=1,ylim=c(-100,100),xlim=c(-100,100),size=1,
                   save=T,path.save='./',filename='tSNE_',date=T,
                   height=9,width=9,res=150,units='in'){

  require(ggplot2)

  if(col.clusters){

    lev = n_distinct(data[,clusters.var])
    if(is.null(palette)){
      mycols <- viRievac::color_cluster(lev)
    } else{
      mycols <- palette
    }

    # data for ploting:
    d = data %>% dplyr::select(vars,louvain = clusters.var) %>% mutate(louvain=factor(louvain))
    colnames(d) = c('tSNE_V1','tSNE_V2','louvain')

    # cluster centroids for labels:
    if(label){
      lc.cent = data %>% group_by_(clusters.var) %>% dplyr::select(vars) %>%
        summarize_all(median)
      colnames(lc.cent) = c('louvain','tSNE_V1','tSNE_V2')

      # ggplot:
      p <- ggplot(d, aes(x = tSNE_V1, y = tSNE_V2, colour = (louvain))) +
        geom_point(alpha = alpha,size=size) + theme_bw() +
        ylim(ylim) + xlim(xlim) +
        scale_color_manual(values=mycols)+
        ggrepel::geom_label_repel(aes(label = louvain),
                                  data = lc.cent) + guides(colour = FALSE)
    }else{
      # ggplot:
      p <- ggplot(d, aes(x = tSNE_V1, y = tSNE_V2, colour = (louvain))) +
        geom_point(alpha = alpha,size=size) +
        blank_theme+
        ylim(ylim) + xlim(xlim) +
        scale_color_manual(values=mycols)
    }

  } else{
    # data for plot:
    d = data %>% dplyr::select(vars)
    colnames(d) = c('tSNE_V1','tSNE_V2')

    # ggplot:
    p <- ggplot(d, aes(x=tSNE_V1, y=tSNE_V2)) +
      geom_point(alpha = alpha,size=size) + theme_bw() + ylim(ylim) + xlim(xlim)
  }

  if(save){
    # create filename:
    filename = paste0(path.save,filename)
    if(col.clusters) filename = paste0(filename,'_with_',lev,"_clusters")
    if(date) filename = paste0(filename,'_',Sys.Date())

    # save in png:
    png(file = paste0(filename,".png"),
        height=height,width=width,res=res,units=units)
    print(p)
    dev.off()
  } else{
    print(p)
  }

}