R stack plot based on value

Question

I want to make a picture with R. I have data like this: 3 Samples and 4 categories, with value A, B and C

      Sam1 Sam2 Sam3
Cat1  A    B;C  C
Cat2  B    A    A;B
Cat3  A;C  C    A;B;C
Cat4  B    A    C

I want to make a plot, with stack colour for the multiple value. The output that I want is in the picture.

Can anyone help? Thank you.

(This solved by Robert Hacken, Thanks).. Another add-on that I want is add notes on the side For G1 has note D1 on the side, and so on... Is it possible?

enter image description here

Thank you.

Answer 1

With visualizations like this, I usually find it easiest to just draw them:

dat <- read.table(text='Sam1 Sam2 Sam3
Cat1  A    B;C  C
Cat2  B    A    A;B
Cat3  A;C  C    A;B;C
Cat4  B    A    C')

let.col <- c(A='red', B='#5b9bd5', C='#70ad47')
# width of the space between squares; square side + sep = 1, so sep=.2 means
#   that the square's side will be four times the empty space
sep <- .2

par(mar = rep(0, 4))
frame()
plot.window(c(0, ncol(dat) + 2), c(nrow(dat) + 1, 0), asp=1)

for (i in 0:nrow(dat)) {
  for (j in 0:ncol(dat)) {
    # first row -- Sx labels
    if (i == 0) {
      if (j > 0) text(j + .5, .5, paste0('S', j))
    # first column -- Gx labels
    } else if (j == 0) {
      if (i > 0) text(.5, i + .5, paste0('G', i))
    # stacked colours
    } else {
      # colors for the current stack
      cols.ij <- let.col[unlist(strsplit(dat[i, j], ';'))]
      for (k in seq_along(cols.ij)) {
        rect(j + sep/2, 
             # rectangle's top goes down for subsequent colors in the stack
             i + (1-sep) * (k-1) / length(cols.ij) + sep/2, 
             j + 1 - sep/2, 
             i + 1 - sep/2, 
             col=cols.ij[k])
      }
    }
  }
}

We could use legend() for legend but its customizability is limited and doing it by hand is not so much work:

# legend top left coordinates
leg.x <- ncol(dat) + 1.4
leg.y <- 1 + mar/2
# size of the square in legend
leg.sq <- .4
# space between squares in legend
leg.sep <- mar

for (i in seq_along(let.col)) {
  rect(leg.x, leg.y, leg.x + leg.sq, leg.y + leg.sq, col=let.col[i])
  text(leg.x + leg.sq*1.4, leg.y + leg.sq/2, names(let.col)[i])
  leg.y <- leg.y + leg.sq + leg.sep
}

To add a column with notes you can modify the code like this:

par(mar = rep(0, 4))
frame()
plot.window(c(0, ncol(dat) + 3), c(nrow(dat) + 1, 0), asp=1)
col.labels <- c(paste0('S', seq_len(ncol(dat))), 'Note')
notes <- c('D1', 'note2%', 'D3', 'D4')

for (i in 0:nrow(dat)) {
  for (j in 0:(ncol(dat)+1)) {
    # first row -- Sx labels
    if (i == 0) {
      if (j > 0) text(j + .5, .5, col.labels[j])
    # first column -- Gx labels
    } else if (j == 0) {
      if (i > 0) text(.5, i + .5, paste0('G', i))
    # stacked colours
    } else {
      # colors for the current stack
      if (j <= ncol(dat)) {
        cols.ij <- let.col[unlist(strsplit(dat[i, j], ';'))]
        for (k in seq_along(cols.ij)) {
          rect(j + sep/2, 
               # rectangle's top goes down for subsequent colors in the stack
               i + (1-sep) * (k-1) / length(cols.ij) + sep/2, 
               j + 1 - sep/2, 
               i + 1 - sep/2, 
               col=cols.ij[k])
        }
      # notes
      } else {
        text(j + .3, i + .5, notes[i], adj=0)
      }
    }
  }
}

This is without the legend but it can be added the same way as before, just increase leg.x to make space for the notes.