R/dsm_plot.R

In chavezlab/csnl: CSN Lab Helper Functions

#' Off-diagonal Plotting Function for Dissimlarity Matricies
#'
#' This function will plot the off-diagonal elements of a dissmilarity matrix.
#' @param dsm a (dis)similarity matrix
#' @param col_n number of colors used in palette
#' @param color_dir direction of the color ramp. 1 == forward, -1 == reverse
#' @param rev_fac logical indicating whether to reverse the factor level order
#' @param melt logical indicating whether or not to melt the matrix into a data frame prior to plotting
#' @author Robert S. Chavez
#' @export
#' @examples
#' cars_dsm <- 1-cor(mtcars)
#' dsm_plot(cars_dsm)

dsm_plot <- function(dsm, col_n = 8, color_dir = 1, rev_fac=FALSE, melt=TRUE){

  library(ggplot2)
  library(colorRamps)
  library(viridis)

  if(melt==TRUE){
    df <- dsm_mask(dsm)
    }

  if(rev_fac==FALSE){
    df <- df[which(is.na(df[,3])==FALSE),]
    df[,1] <- factor(df[,1])
    df[,2] <- factor(df[,2])
    df$Var1 <- df[,1]
    df$Var2 <- df[,2]
    df$value <- df[,3]
    mytheme <- theme(panel.grid.minor=element_blank(), panel.grid.major=element_blank())
    ggplot(df, aes(Var1,Var2,fill=value)) + geom_raster() + theme_minimal() + mytheme +
      scale_fill_gradientn(colors = magma(col_n, direction = color_dir),name = "Dissimilarity") + xlab("") + ylab("")
  }

  else{
    df <- dsm[which(is.na(df[,3])==FALSE),]
    df[,1] <- factor(df[,1])
    df[,2] <- factor(df[,2])
    df[,2] <- factor(df[,2],levels = rev(levels(df[,2])))
    df$Var1 <- df[,1]
    df$Var2 <- df[,2]
    df$value <- df[,3]
    mytheme <- theme(panel.grid.minor=element_blank(), panel.grid.major=element_blank(), axis.text.x = element_text(angle = 300, hjust = 0))
    ggplot(df, aes(Var1,Var2,fill=value)) + geom_raster() + theme_minimal() + mytheme +
      scale_fill_gradientn(colors = magma(col_n, direction = color_dir),name = "Dissimilarity") + xlab("") + ylab("")
  }
}