Plots the correlation among the columns of a numeric matrix.

We assume that this is a sample x gene expression matrix, but it can (of course) be any numeric matrix of your choosing. The column names appear in the main diagonal of the plot. Note that you might prefer the corrplot package for similar functionality, and this functionality is intentionally named different from that..

corplot(
  E,
  title,
  cluster = FALSE,
  col.point = "#00000066",
  diag.distro = TRUE,
  smooth.scatter = nrow(E) > 400,
  max.cex.cor = NULL,
  ...
)

Arguments

E

the matrix used to plot a pairs correlation plot. The vectors used to assess all pairwise correlation should be in the columns of the matrix.

title

The title of the plot

cluster

logical indicating whether or not to shuffle genes around into some clustering.

col.point

the color of the points in the scatterplots

diag.distro

show the distribution of values on the diagnols?

smooth.scatter

boolean to indicate wether to use a normal scatter, or a graphics::smoothScatter(). Defaults to TRUE if nrow(E) > 400

max.cex.cor

the numeric value defining the maximum text size (cor) in the correlation panel. By default there is no limit on the maximum text size and the text size is calculated with 0.8 / strwidth(text). With max.cex.cor defined the text size is calculated as min(0.8 / strwidth(text), max.cex.cor).

...

pass through arguments to internal panel functions

Value

nothing, just creates the plot

Details

TODO: Add with.signature parameter to allow a box to plot the signature score of all genes in E.

See also

The corrplot package

Examples

x <- matrix(rnorm(1000), ncol=5)
corplot(x)
#> Warning: argument 1 does not name a graphical parameter
#> Warning: argument 1 does not name a graphical parameter
#> Warning: argument 1 does not name a graphical parameter
#> Warning: argument 1 does not name a graphical parameter
#> Warning: argument 1 does not name a graphical parameter
#> Warning: argument 1 does not name a graphical parameter
#> Warning: argument 1 does not name a graphical parameter
#> Warning: argument 1 does not name a graphical parameter
#> Warning: argument 1 does not name a graphical parameter
#> Warning: argument 1 does not name a graphical parameter
#> Warning: argument 1 does not name a graphical parameter
#> Warning: argument 1 does not name a graphical parameter
#> Warning: argument 1 does not name a graphical parameter
#> Warning: argument 1 does not name a graphical parameter
#> Warning: argument 1 does not name a graphical parameter