Chapter 13 Smoothing in high dimensions

In situations where you are plotting a very large matrix, often the heatmap becomes obscured by noise due to the sheer amount of information being presented relative to the number of pixels available.

To address this common issue, we have allowed for smoothing by summarizing values within a cluster by the median value. This can be achieved using the smooth.heat argument.

gears <- paste(mtcars$gear, "gears")

set.seed(2016113)
superheat(mtcars,
          # scale the matrix columns
          scale = TRUE,
          
          # cluster by gears
          membership.rows = gears,
          
          # place each variable in its own cluster
          membership.cols = 1:ncol(mtcars),
          bottom.label = "variable",
          
          # smooth the heatmap within clusters
          smooth.heat = TRUE)

## Warning: Column `rclust` joining factors with different levels, coercing to
## character vector

## Warning: Column `cclust` joining factors with different levels, coercing to
## character vector