R/plot_pca_paint_gene_repel.R

In graeberlab-ucla/glab.library: Data Analysis Functions

#' Plot PCA Paint Gene
#'
#' Plots PCA from scores file (output of PCA_from_file)
#'
#' plot_pca_paint_gene differs from plot_pca in that it uses gradient coloring of points based on the expression values of a gene
#' plot_pca_paint_gene_repel uses geom_text_repel
#'
#' @param file File containing scores matrix
#' @param info.name Vector of sample names
#' @param info.type Vector of sample types in the same order
#' @param title Title of the plot
#' @param labels default=T
#' @param PCx,PCy PCs to display
#' @param ellipse Construct confidence region based on groups in info.type, default = T
#' @param conf default = 0.95
#' @param density plot x-y density plots
#' @param fliph,flipv flip plot hoirzontally or vertically
#'
# @importFrom ggplot2 ggplot aes aes_string element_rect element_text geom_point geom_text labs margin theme theme_bw
#'
#' @import ggplot2
#' @import ggpubr
#' @import ggrepel
#' @import vegan
#' @import RColorBrewer
#'
#' @export
#'

# file = "TOIL_TCGA_UVM_norm_protein.coding_log_non.zero_prcomp_scores.txt"
# info.name = human.info$sample.short3
# info.type = human.info$BAP1.Altered
# gene = "JUN"
# PCx = "PC1"
# PCy = "PC2"
# labels=F
# title=""

# file = "UVM_cell_lines_Kim_rsem_genes_upper_norm_counts_protein.coding_log_prcomp_scores.txt"
# gene = "CGAS"
# PCx = "PC1"
# PCy = "PC2"
# labels=F
# title=""
# setwd("/Users/tgraeber/Dropbox/glab/collab f/Kim Paraiso/PCA of UVM RNAseq/")

# file = proj_name_fake
# gene = "ASCL2"
# PCx = "PC1"
# PCy = "PC2"
# labels=F
# title=""
# sDev_file_exists = F
# setwd("/Users/tgraeber/Dropbox/glab/collab f/Kim Paraiso/PCA of UVM RNAseq/")

# file = "melanoma.geneexp_prcomp_scores.txt"
# file = "melanoma.geneexp_modnames_prcomp_scores.txt"

#plot_pca_paint_gene = function(file, info.name, info.type, gene = "JUN", title = "", labels = TRUE, PCx="PC1", PCy="PC2", ellipse = F, conf = 0.95, density=F,
#                               fliph = F, flipv = F){
plot_pca_paint_gene_repel = function(file, gene = "JUN", title = "", labels = TRUE, PCx="PC1", PCy="PC2", ellipse = F, conf = 0.95, density=F,
                                 fliph = F, flipv = F, sDev_file_exists = TRUE){
    #Input: PCA scores file to be ploted
  ##process pca output and adds groupings
  require(ggplot2);require(ggpubr);require(ggrepel)
  require(vegan)
  require(RColorBrewer)
  title = paste0(title," ",gene)
  table <- read.table(file, header = TRUE)
  #table$type = info.type[match(table$Score, info.name)]
  #table$color = info.color[match(table$Score, info.name)]

  file.gexp = gsub("_prcomp_scores", "", file)
  table.loadings.t = read.delim(file.gexp, header = FALSE, sep="\t")
  table.loadings.t2 <- rbind(table.loadings.t[1,], table.loadings.t[table.loadings.t$V1 == gene,])
  table.loadings <- as.data.frame(t(table.loadings.t2))
  colnames(table.loadings) <- c("sample", "color")
  table.loadings <- table.loadings[-1,]

  table = merge(table, table.loadings, by.x="Score", by.y="sample")

  if (fliph==T){table[,PCx] = table[,PCx]*-1}
  if (flipv==T){table[,PCy] = table[,PCy]*-1}

  table$color <- as.numeric(as.character(table$color))
  #class(table$color)
  #class(table)
  min = min(table$color)
  max = max(table$color)
#  min = min(as.numeric(as.matrix(table$color)))
#  max = max(as.numeric(as.matrix(table$color)))

  colorpalette="RdYlBu"
  #colorpalette="RdBu"

  if (sDev_file_exists) {
    sdev = read.delim(paste0(gsub("scores.txt","",file),"sdev.txt"))
    sdev$var = unlist(sdev^2)
    sdev$pve = unlist(round(sdev$var/sum(sdev$var) * 100, digits = 2))
    rownames(sdev) = paste0("PC",seq(1,nrow(sdev)))
  } else {
    sdev = as.data.frame(rep("-",10))
    rownames(sdev) = paste0("PC",seq(1,nrow(sdev)))
    colnames(sdev) = "pve"
  }

  #pcx.y <- ggplot(table, aes_string(x=PCx,y=PCy)) +geom_point(size = I(3), aes(color = factor(type))) +
  pcx.y <- ggplot(table, aes_string(x=PCx,y=PCy)) +geom_point(size = I(3), aes(fill = color), colour="black",pch=21) +
    scale_fill_gradientn("",colours=c(rev(brewer.pal(9,colorpalette))),limits=c(min,max)) +
          theme(legend.position="right",plot.title=element_text(size=30),legend.text=element_text(size=22),
          legend.title=element_text(size=20),axis.title=element_text(size=30),legend.background = element_rect(),
          axis.text.x = element_text(margin = margin(b=-2)),axis.text.y = element_text(margin = margin(l=-14)))+
    guides(color=guide_legend(title=gene))+
    labs(title = title,
         x = paste0(PCx," (", sdev$pve[match(PCx, rownames(sdev))], "%)"),
         y = paste0(PCy," (", sdev$pve[match(PCy, rownames(sdev))], "%)"))+
    theme_bw(base_size=18)+
    if(labels==TRUE){geom_text_repel(data = table, mapping = aes(label = Score), check_overlap = TRUE, size = 3)}

  if(ellipse==TRUE){
    plot(table[,c(PCx, PCy)], main=title)
    ord = ordiellipse(table[,c(PCx, PCy)],table$type, kind = "sd", conf = conf)

    cov_ellipse<-function (cov, center = c(0, 0), scale = 1, npoints = 100)
    {
      theta <- (0:npoints) * 2 * pi/npoints
      Circle <- cbind(cos(theta), sin(theta))
      t(center + scale * t(Circle %*% chol(cov)))
    }

    df_ell <- data.frame(matrix(ncol = 0, nrow = 0))
    for(g in (droplevels(table$type))){
      df_ell <- rbind(df_ell, cbind(as.data.frame(with(table[table$type==g,],
                                                       cov_ellipse(ord[[g]]$cov,ord[[g]]$center,ord[[g]]$scale)))
                                    ,type=g))
    }

    pcx.y2 = pcx.y + geom_path(data=df_ell, aes(x=df_ell[,PCx], y=df_ell[,PCy], colour = type), size=1, linetype=1)
    print(pcx.y2)
    # if(density==TRUE){
    #
    #   # Marginal density plot of x (top panel) and y (right panel)
    #   xplot <- ggdensity(table, PCx, fill = "type")+ clean_theme()
    #   yplot <- ggdensity(table, PCy, fill = "type")+ rotate()+ clean_theme()
    #   # Arranging the plot
    #   print(ggarrange(xplot, NULL, pcx.y2, yplot,
    #                   ncol = 2, nrow = 2,  align = "hv",
    #                   widths = c(2, 1), heights = c(1, 2),
    #                   common.legend = TRUE))
    # }
    # else{
    #   print(pcx.y2)
    # }
    #
  } else{
    print(pcx.y)
  }
  if(density==TRUE){

    # Marginal density plot of x (top panel) and y (right panel)
    xplot <- ggdensity(table, PCx, fill = "type")+ clean_theme()
    yplot <- ggdensity(table, PCy, fill = "type")+ rotate()+ clean_theme()
       # Arranging the plot
    (ggarrange(xplot, NULL, pcx.y, yplot,
              ncol = 2, nrow = 2,  align = "hv",
              widths = c(2, 1), heights = c(1, 2),
              common.legend = TRUE))
  }
  else{
    print(pcx.y)
  }


}