How do I stop ggplot2 from rotating my matrix 90 degrees?

Question

I'm trying to create a heatmap using ggplot2, but I noticed that it seems to rotate the matrix 90 degrees to the left when I plot it. It's very strange, and using coord_flip() and t() don't work, because they rotate it to the left, not the right (so rather than correcting, they create a heatmap that is rotated 180 degrees). Are there any options or tricks to prevent this? Here is the relevant code:

#this is needed to run custHeat
zeroInterval <- function(mat, colors){
  #modified version of findInterval such that zero is given its own category
  #This function takes intervals as left exclusive, right inclusive.
  #This is mostly so that intervals consisting of a single value will still be represented.
  intervalMat <- matrix(0, nrow=nrow(mat), ncol=ncol(mat))
  j <- 1
  for(i in 1:(length(colors) - 1)){
    if(colors[i] != colors[i+1]){
      intervalMat[mat>colors[i] & mat<=colors[i+1]] <- j
      j <- j + 1
    } else {
      intervalMat[mat==colors[i]] <- j
      j <- j + 1
    }
  }
  return(intervalMat)
}

#this actually plots the heatmap
custHeat <- function(M){

  #create color bins/ranges for skewed matrix
  color_bins <- c(-5, -4, -3, -2, -1, 0, 0, 1)
  colors <- c('#67001F', '#B2182B', '#D6604D', '#F4A582', '#FDDBC7', "#FFFFFF", '#C6DBEF')

  #create complete color palette
  color_palette <- colorRampPalette(colors)(length(color_bins) - 1)

  #This function assigns a number to each matrix value, so that it is colored correctly
  mod_mat <- zeroInterval(random_matrix, color_bins)


  ## remove background and axis from plot
  theme_change <- theme(
    plot.background = element_blank(),
    panel.grid.minor = element_blank(),
    panel.grid.major = element_blank(),
    panel.background = element_blank(),
    panel.border = element_blank(),
    axis.line = element_blank(),
    axis.ticks = element_blank(),
    axis.text.x = element_blank(),
    axis.text.y = element_blank(),
    axis.title.x = element_blank(),
    axis.title.y = element_blank()
  )

  ## output the graphics
  ggplot(melt(mod_mat), aes(x = X1, y = X2, fill = factor(value))) +
    geom_tile(color = "black") +
    scale_fill_manual(values = color_palette, name = "") +
    theme_change
}

##create random matrix, skewed toward negative values
random_matrix <- matrix(runif(100, min = -5, max = 1), nrow = 10)
random_matrix[1,] <- 0 #zeros should be at the top row of the heatmap
custHeat(random_matrix)

Answer 1

You can counteract the 90 degree counter-clockwise rotation of the plotting function by pre-rotating your matrix 90 degrees in the other direction:

## An example matrix
(m <- matrix(1:9, ncol=3))
#      [,1] [,2] [,3]
# [1,]    1    4    7
# [2,]    2    5    8
# [3,]    3    6    9

## The same matrix rotated 90 degrees clockwise
t(m)[,nrow(m):1]
#      [,1] [,2] [,3]
# [1,]    3    2    1
# [2,]    6    5    4
# [3,]    9    8    7

---

Added later:

Some R plotting functions use the same convention as image(), while others do not. (Please feel free to add to this list.)

m <- matrix(1:9, ncol=3)


## ------- These plotting functions DO rotate a matrix --------

## image()
image(m, col=blues9)

## levelplot() -- a lattice equivalent of image()
library(lattice)    
levelplot(m, at=(1:10)-0.5, col.regions=blues9)

## Others
contour(m)
filled.contour(m, color=colorRampPalette(blues9))
persp(m) 
lattice::contourplot(m)
lattice::wireframe(m)  ## Nicely illustrates the logic of the indexing it uses


## ------- These plotting functions DO NOT --------

## imageRaster() -- a graphical primitive used by image(), among other functions 
plot(0:1, 0:1, type="n", xlab="", ylab="")
rasterImage(matrix(blues9, ncol=3), 0,0,1,1, interpolate=FALSE)

## grid.raster() -- imageRaster()'s counterpart in the grid graphical system
library(grid)
grid.raster(matrix(blues9, ncol=3), interpolate=FALSE)

## plot(raster()) in raster package
library(raster)
plot(raster(m), col=blues9)