R/drawXYCorr.R

In cnsb-boston/Omics_Notebook: What the package does (short line)

#-------------------------------------------------
#' Draw XY Correlation Plot
#'
#' This function generates correlation plots
#' 
#' @param item_list a list of tibbles
#' @param item_name a name for the items
#' @param outputpath output file path for plots
#' @param file_name suffix for plot filename
#' 
#' @examples
#' 
#' @import ggplot2
#' @export
drawXYCorr <- function(item_list, item_name, outputpath=output_plots_path, file_name="", subset_genes=FALSE){
  
  plotXYCorr <- function(sublist=NULL, expanded_title=NULL){
    for (j in 1:(length(item_list)-1)){
      for (k in (j+1):length(item_list)){
        # make data to plot
        plot_data <- merge(item_list[[j]], item_list[[k]], by.x=item_name, by.y=item_name)
        colnames(plot_data) <- c(item_name, names(item_list)[j], names(item_list)[k])
        title=paste0("Avg. ",item_name, " ", file_name)
        if(!is.null(sublist)){
          plot_data <- plot_data[which(plot_data[,item_name] %in% sublist),]
          if(!is.null(expanded_title)) title=paste0(title," in ",expanded_title,": \n",
                                          names(item_list)[j]," vs. ",names(item_list)[k])
        }
        if(nrow(plot_data)==0){ next; }
        # density colors
        x<-grDevices::densCols(plot_data[,2], plot_data[,3],colramp=grDevices::colorRampPalette(c("black","white")))
        plot_data$Density <- grDevices::col2rgb(x)[1,] + 1L
        # make plot
        corr_coef <- cor(plot_data[,2], plot_data[,3], method="pearson");
        label<-paste("italic(r) == ",round(corr_coef, digits=2), sep="");
        plot <- ggplot(data=plot_data, aes(x=plot_data[,2], y=plot_data[,3], color=Density)) + 
          geom_point() + viridis::scale_color_viridis(direction=-1) + labs(x=names(item_list)[j], y=names(item_list)[k]) +
          labs(title=title) +
          theme_bw() + annotate("text",x=-Inf, y=Inf, label=label, color="black", vjust=1.5, hjust=-0.4 , parse=TRUE) +
          geom_smooth(method=lm, se=FALSE, color="red", formula=y~x)
        print(plot+theme(legend.position="none"))
        gridExtra::grid.arrange(g_legend(plot))
      }
    }
  }

  output_filename<-file.path(outputpath,paste("Correlation_Plots_",item_name,"_",file_name,".pdf", sep=""))
  pdf(output_filename, width=3, height=3 )

  plotXYCorr()

  # Repeat for subset genes
  if( class(subset_genes)!="logical"){
    for( i in 1:length(subset_genes) ){ try({
      plotXYCorr(subset_genes[[i]],names(subset_genes)[i])
    }) }
  }
  dev.off()
}