How to create a time series plot in the style of a horizontal stacked bar plot in r

Question

I would like to create a horizontal ‘stacked bar’ type plot in which date runs along the x-axis and my samples appear as bars on the y-axis. In the simple example below, I have three samples (a, b, c) each containing three values (0, 1, 2). I would like the horizontal bar to be coloured based on the value at each time step along the x-axis, so that I end up with three horizontal bars (one for each sample) that run from my first to last time point and contain a series of blocks with colours that relate to the different values.

For example, say I want value 0 to be blue, value 1 to be yellow and value 2 to be red: for sample a, the first two days of the trace would be blue, then the next two days would be yellow, followed by a single blue and so on……

Example data:

df <- structure(list(date = c("30/04/2011", "01/05/2011", "02/05/2011", "03/05/2011", "04/05/2011", "05/05/2011", "06/05/2011", "07/05/2011", "08/05/2011", "09/05/2011", "10/05/2011", "11/05/2011", "12/05/2011", "13/05/2011", "14/05/2011", "15/05/2011", "16/05/2011", "17/05/2011", "18/05/2011", "19/05/2011", "20/05/2011", "21/05/2011", "22/05/2011", "23/05/2011", "24/05/2011", "25/05/2011", "26/05/2011", "27/05/2011", "28/05/2011", "29/05/2011", "30/05/2011", "31/05/2011", "01/06/2011", "02/06/2011", "03/06/2011", "04/06/2011", "05/06/2011", "06/06/2011", "07/06/2011", "08/06/2011", "09/06/2011", "10/06/2011", "11/06/2011", "12/06/2011", "13/06/2011", "14/06/2011", "15/06/2011", "16/06/2011", "17/06/2011", "18/06/2011", "19/06/2011", "20/06/2011", "21/06/2011", "22/06/2011", "23/06/2011", "24/06/2011", "25/06/2011", "26/06/2011", "27/06/2011", "28/06/2011", "29/06/2011", "30/06/2011", "01/07/2011", "02/07/2011", "03/07/2011", "04/07/2011", "05/07/2011", "06/07/2011", "07/07/2011", "08/07/2011", "09/07/2011", "10/07/2011", "11/07/2011", "12/07/2011", "13/07/2011", "14/07/2011", "15/07/2011", "16/07/2011", "17/07/2011", "18/07/2011", "19/07/2011", "20/07/2011", "21/07/2011", "22/07/2011", "23/07/2011", "24/07/2011"), a = c(0L, 0L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L), b = c(0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 1L), c = c(1L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L)), .Names = c("date", "a", "b", "c"), class = "data.frame", row.names = c(NA, -86L))

head(df)
#         date a b c
# 1 30/04/2011 0 0 1
# 2 01/05/2011 0 1 1
# 3 02/05/2011 1 1 0
# 4 03/05/2011 1 0 0
# 5 04/05/2011 0 0 0

This must be a really easy thing to achieve but I can’t get my head around it (i.e. bar plot doesn't seem to work for this). Any help would be appreciated. Thanks!

Answer 1

For a ggplot2 plot first convert df to long form (using melt from the reshape2 package), convert the date column to "Date" class and the value column to a factor and then use geom_tile:

library(ggplot2)
library(reshape2)

long <- melt(df, measure.var = 2:4)
long <- transform(long, date = as.Date(long$date, "%d/%m/%Y"), value = factor(value))

ggplot(long, aes(date, variable)) + 
   geom_tile(aes(fill = value)) + 
   scale_fill_manual(values = c("blue", "yellow", "red"))

Answer 2

This is very manual, but I think it answers your question. To my knowledge there is not a function that does this for you -- but I could very likely be wrong. I just used polygon to draw the boxes for each group. NOTE: You need to change your date field to a Date class.

dat$date <- as.Date(dat$date, "%d/%m/%Y")

plot(dat$a~dat$date, type = "n", yaxt = "n", ylab = "", 
     xlab = "", bty = "n", ylim = c(0, 4))
draw.box <- function(y, x1, x2, h, col) {
  polygon(x = c(x1, x1, x2, x2), 
          y = c(y - h/2, y + h/2, y + h/2, y - h/2),
          col = col, border = col)
}

for (j in c("a", "b", "c")) {
  for (i in 2:nrow(dat)) {
    bcol <- switch(as.character(dat[(i - 1), j]),
                   "0" = "red",
                   "1" = "blue",
                   "2" = "yellow")
    yloc <- switch(j,
                   "a" = 3,
                   "b" = 2,
                   "c" = 1)
    draw.box(y = yloc, 
             h = 0.75, 
             col = bcol, 
             x1 = dat[(i - 1), "date"], 
             x2 = dat[i, "date"])
  }
}

axis(side = 2, at = 3:1, labels = c("A", "B", "C"), 
     tick = FALSE, las = 2)

Here the last value is not plotted, because there is no "end date" to bound the bar.