heatmap {tempmva} | R Documentation |
A heat map is a false color image with a dendrogram added to the left side and to the top. Typically reordering of the rows and columns according to some set of values (row or column means) within the restrictions imposed by the dendrogram is carried out.
heatmap(x, Rowv, Colv, distfun = dist, add.expr, scale=c("row", "column", "none"), na.rm = TRUE, ...)
x |
numeric matrix of the values to be plotted. |
Rowv |
Either a dendrogram or a vector of values
used to reorder the row dendrogram. |
Colv |
Either a dendrogram or a vector of values used to reorder the column dendrogram. |
distfun |
function used to compute the distance (dissimilarity)
between both rows and columns. Defaults to dist . |
add.expr |
expression that will be evaluated after the call to image. Can be used to add components to the plot. |
scale |
character indicating if the values should be centered and
scaled in either the row direction or the column direction, or
none. The default is "row" . |
na.rm |
logical indicating whether NA 's should be removed |
... |
additional arguments passed on to image ,
e.g. col specifying the colors. |
If either Rowv
or Colv
are dendrograms they are honored
(and not reordered). If either is a vector then the apropriate
dendrogram is reordered according to the supplied values, subject to
the constraints imposed by the dendrogram. If either is missing, as
by default, then the ordering of the corresponding dendrogram is by
the mean value of the rows/columns.
By default the rows are scaled to have mean zero and standard deviation one. There is some empirical evidence from genomic plotting that this is useful.
The default colors are not pretty. Consider using RColorBrewer.
No value is returned. The function is called for the side effect of producing a picture.
Andy Liaw, original, R. Gentleman, revisions
set.seed(132) x <- matrix(runif(1000), 50, 20) heatmap(x, col = topo.colors(32), main = "Random U[0,1] heatmap") data(volcano) ## Volcano is not recognizable, but at least not random heatmap(volcano, col = gray(0:64/64))