How to plot dataframe in R as a heatmap/grid?

Question

I would be extremely grateful for some help with R. I would like to plot a dataframe of gridded data (like for like running down the diagonal, from top left to bottom right). I've seen quite a few examples using ggplot2, however, I simply lack the experience necessary with R to manipulate the data structures; I've been programming in LISP and Java for years yet my head won't get around R :-(

The data looks like this:

                    tension    cluster     migraineNoAura          migraineAura
tension                  NA          1.5        6.960453e+00          3.596953
cluster        1.943113e+08           NA                  NA                NA
migraineNoAura 8.462798e+00           NA                  NA          7.499999
migraineAura   2.833333e+00           NA        7.148313e+07                NA

This is only a small subset, it's a 60x60 data frame. Notice the NAs.

I'm hoping for a 60x60 grid, coloured by the value and the x and y labeled using the names from the data frame.

Answer 1

First, you need to format your data frame from wide format to long format. The following is an example using tidyverse to format the data frame.

library(tidyverse)

dt2 <- dt %>%
  rownames_to_column() %>%
  gather(colname, value, -rowname)
head(dt2)
#          rowname colname        value
# 1        tension tension           NA
# 2        cluster tension 1.943113e+08
# 3 migraineNoAura tension 8.462798e+00
# 4   migraineAura tension 2.833333e+00
# 5        tension cluster 1.500000e+00
# 6        cluster cluster           NA

Now we are ready to use the ggplot2 to plot the heatmap using geom_tile.

ggplot(dt2, aes(x = rowname, y = colname, fill = value)) +
  geom_tile()