Description Usage Arguments Details Value Note Author(s) See Also Examples
A heat map is a false color image (basically
image(t(x))
) with a dendrogram added to the left side
and/or 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.
For now the only difference between gplots::heatmap.2 is the addition of the col.srt argument, which allows you to rotate column labels.
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# dendrogram control
Rowv = TRUE,
Colv=if(symm)"Rowv" else TRUE,
distfun = dist,
hclustfun = hclust,
dendrogram = c("both","row","column","none"),
symm = FALSE,
# data scaling
scale = c("none","row", "column"),
na.rm=TRUE,
# image plot
revC = identical(Colv, "Rowv"),
add.expr,
# mapping data to colors
breaks,
symbreaks=min(x < 0, na.rm=TRUE) || scale!="none",
# colors
col="heat.colors",
# block sepration
colsep,
rowsep,
sepcolor="white",
sepwidth=c(0.05,0.05),
# cell labeling
cellnote,
notecex=1.0,
notecol="cyan",
na.color=par("bg"),
# level trace
trace=c("column","row","both","none"),
tracecol="cyan",
hline=median(breaks),
vline=median(breaks),
linecol=tracecol,
# Row/Column Labeling
margins = c(5, 5),
ColSideColors,
RowSideColors,
cexRow = 0.2 + 1/log10(nr),
cexCol = 0.2 + 1/log10(nc),
labRow = NULL,
labCol = NULL,
col.srt = NULL,
# color key + density info
key = TRUE,
keysize = 1.5,
density.info=c("histogram","density","none"),
denscol=tracecol,
symkey = min(x < 0, na.rm=TRUE) || symbreaks,
densadj = 0.25,
# plot labels
main = NULL,
xlab = NULL,
ylab = NULL,
# plot layout
lmat = NULL,
lhei = NULL,
lwid = NULL,
# extras
...
)
|
x |
numeric matrix of the values to be plotted. |
Rowv |
determines if and how the row dendrogram should be
reordered. By default, it is TRUE, which implies dendrogram is
computed and reordered based on row means. If NULL or FALSE, then no
dendrogram is computed and no reordering is done. If a
|
Colv |
determines if and how the column dendrogram should be
reordered. Has the options as the |
distfun |
function used to compute the distance (dissimilarity)
between both rows and columns. Defaults to |
hclustfun |
function used to compute the hierarchical clustering
when |
dendrogram |
character string indicating whether to draw 'none', 'row', 'column' or 'both' dendrograms. Defaults to 'both'. However, if Rowv (or Colv) is FALSE or NULL and dendrogram is 'both', then a warning is issued and Rowv (or Colv) arguments are honoured. |
symm |
logical indicating if |
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 |
na.rm |
logical indicating whether |
revC |
logical indicating if the column order should be
|
add.expr |
expression that will be evaluated after the call to
|
breaks |
(optional) Either a numeric vector indicating the
splitting points for binning |
symbreaks |
Boolean indicating whether breaks should be
made symmetric about 0. Defaults to |
col |
colors used for the image. Defaults to heat colors
( |
colsep, rowsep, sepcolor |
(optional) vector of integers indicating
which columns or rows should be separated from the preceding columns
or rows by a narrow space of color |
sepwidth |
(optional) Vector of length 2 giving the width (colsep) or height (rowsep) the separator box
drawn by colsep and rowsep as a function of the width (colsep) or
height (rowsep) of a cell. Defaults to |
cellnote |
(optional) matrix of character strings which will be placed within each color cell, e.g. p-value symbols. |
notecex |
(optional) numeric scaling factor for |
notecol |
(optional) character string specifying the color for
|
na.color |
Color to use for missing value ( |
trace |
character string indicating whether a solid "trace" line should be drawn across 'row's or down 'column's, 'both' or 'none'. The distance of the line from the center of each color-cell is proportional to the size of the measurement. Defaults to 'column'. |
tracecol |
character string giving the color for "trace" line. Defaults to "cyan". |
hline, vline, linecol |
Vector of values within cells where a
horizontal or vertical dotted line should be drawn. The color of
the line is controlled by |
margins |
numeric vector of length 2 containing the margins
(see |
ColSideColors |
(optional) character vector of length |
RowSideColors |
(optional) character vector of length |
cexRow, cexCol |
positive numbers, used as |
labRow, labCol |
character vectors with row and column labels to
use; these default to |
col.srt |
If a numeric value, the number of degrees by which to rotate the column labels. Default is NULL for vertical labels. |
key |
logical indicating whether a color-key should be shown. |
keysize |
numeric value indicating the size of the key |
density.info |
character string indicating whether to superimpose a 'histogram', a 'density' plot, or no plot ('none') on the color-key. |
denscol |
character string giving the color for the density
display specified by |
symkey |
Boolean indicating whether the color key should be
made symmetric about 0. Defaults to |
densadj |
Numeric scaling value for tuning the kernel width when
a density plot is drawn on the color key. (See the |
main, xlab, ylab |
main, x- and y-axis titles; defaults to none. |
lmat, lhei, lwid |
visual layout: position matrix, column height, column width. See below for details |
... |
additional arguments passed on to |
If either Rowv
or Colv
are dendrograms they are honored
(and not reordered). Otherwise, dendrograms are computed as
dd <- as.dendrogram(hclustfun(distfun(X)))
where X
is
either x
or t(x)
.
If either is a vector (of “weights”) then the appropriate
dendrogram is reordered according to the supplied values subject to
the constraints imposed by the dendrogram, by reorder(dd,
Rowv)
, in the row case.
If either is missing, as by default, then the ordering of the
corresponding dendrogram is by the mean value of the rows/columns,
i.e., in the case of rows, Rowv <- rowMeans(x, na.rm=na.rm)
.
If either is NULL
, no reordering will be done for
the corresponding side.
If scale="row"
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 range from red to white (heat.colors
) and
are not pretty. Consider using enhancements such
as the RColorBrewer package,
http://cran.r-project.org/src/contrib/PACKAGES.html#RColorBrewer
to select better colors.
By default four components will be displayed in the plot. At the top
left is the color key, top right is the column dendogram, bottom left
is the row dendogram, bottom right is the image plot. When
RowSideColor or ColSideColor are provided, an additional row or column
is inserted in the appropriate location. This layout can be
overriden by specifiying appropriate values for lmat
,
lwid
, and lhei
. lmat
controls the relative
postition of each element, while lwid
controls the column
width, and lhei
controls the row height. See the help page for
layout
for details on how to use these
arguments.
Invisibly, a list with components
rowInd |
row index permutation vector as returned by
|
colInd |
column index permutation vector. |
call |
the matched call |
rowMeans, rowSDs |
mean and standard deviation of each row: only
present if |
colMeans, colSDs |
mean and standard deviation of each column: only
present if |
carpet |
reordered and scaled 'x' values used generate the main 'carpet' |
rowDendrogram |
row dendrogram, if present |
colDendrogram |
column dendrogram, if present |
breaks |
values used for color break points |
col |
colors used |
vline |
center-line value used for column trace, present only if
|
hline |
center-line value used for row trace, present only if
|
colorTable |
A three-column data frame providing the lower and upper bound and color for each bin |
The original rows and columns are reordered in any case to
match the dendrogram, e.g., the rows by
order.dendrogram(Rowv)
where Rowv
is the
(possibly reorder()
ed) row dendrogram.
heatmap.3()
uses layout
and draws the
image
in the lower right corner of a 2x2 layout.
Consequentially, it can not be used in a multi column/row
layout, i.e., when par(mfrow= *)
or (mfcol= *)
has been called.
Andy Liaw, original; R. Gentleman, M. Maechler, W. Huber, G. Warnes heatmap.2, Levi Waldron heatmap.3.
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data(mtcars)
x <- as.matrix(mtcars)
rc <- rainbow(nrow(x), start=0, end=.3)
cc <- rainbow(ncol(x), start=0, end=.3)
##
## demonstrate the effect of row and column dendogram options
##
heatmap.3(x) ## default - dendrogram plotted and reordering done.
heatmap.3(x, dendrogram="none") ## no dendrogram plotted, but reordering done.
heatmap.3(x, dendrogram="row") ## row dendrogram plotted and row reordering done.
heatmap.3(x, dendrogram="col") ## col dendrogram plotted and col reordering done.
heatmap.3(x, keysize=2) ## default - dendrogram plotted and reordering done.
heatmap.3(x, Rowv=FALSE, dendrogram="both") ## generate warning!
heatmap.3(x, Rowv=NULL, dendrogram="both") ## generate warning!
heatmap.3(x, Colv=FALSE, dendrogram="both") ## generate warning!
##
## Show effect of z-score scaling within columns, blue-red color scale
##
hv <- heatmap.3(x, col=bluered, scale="column", tracecol="#303030")
###
## Look at the return values
###
names(hv)
## Show the mapping of z-score values to color bins
hv$colorTable
## Extract the range associated with white
hv$colorTable[hv$colorTable[,"color"]=="#FFFFFF",]
## Determine the original data values that map to white
whiteBin <- unlist(hv$colorTable[hv$colorTable[,"color"]=="#FFFFFF",1:2])
rbind(whiteBin[1] * hv$colSDs + hv$colMeans,
whiteBin[2] * hv$colSDs + hv$colMeans )
##
## A more decorative heatmap, with z-score scaling along columns
##
hv <- heatmap.3(x, col=cm.colors(255), scale="column",
RowSideColors=rc, ColSideColors=cc, margin=c(5, 10),
xlab="specification variables", ylab= "Car Models",
main="heatmap(<Mtcars data>, ..., scale=\"column\")",
tracecol="green", density="density")
## Note that the breakpoints are now symmetric about 0
data(attitude)
round(Ca <- cor(attitude), 2)
symnum(Ca) # simple graphic
# with reorder
heatmap.3(Ca, symm=TRUE, margin=c(6, 6), trace="none" )
# without reorder
heatmap.3(Ca, Rowv=FALSE, symm=TRUE, margin=c(6, 6), trace="none" )
## Place the color key below the image plot
heatmap.3(x, lmat=rbind( c(0, 3), c(2,1), c(0,4) ), lhei=c(1.5, 4, 2 ) )
## Place the color key to the top right of the image plot
heatmap.3(x, lmat=rbind( c(0, 3, 4), c(2,1,0 ) ), lwid=c(1.5, 4, 2 ) )
## For variable clustering, rather use distance based on cor():
data(USJudgeRatings)
symnum( cU <- cor(USJudgeRatings) )
hU <- heatmap.3(cU, Rowv=FALSE, symm=TRUE, col=topo.colors(16),
distfun=function(c) as.dist(1 - c), trace="none")
## The Correlation matrix with same reordering:
hM <- format(round(cU, 2))
hM
# now with the correlation matrix on the plot itself
heatmap.3(cU, Rowv=FALSE, symm=TRUE, col=rev(heat.colors(16)),
distfun=function(c) as.dist(1 - c), trace="none",
cellnote=hM)
## genechip data examples
## Not run:
library(affy)
data(SpikeIn)
pms <- SpikeIn@pm
# just the data, scaled across rows
heatmap.3(pms, col=rev(heat.colors(16)), main="SpikeIn@pm",
xlab="Relative Concentration", ylab="Probeset",
scale="row")
# fold change vs "12.50" sample
data <- pms / pms[, "12.50"]
data <- ifelse(data>1, data, -1/data)
heatmap.3(data, breaks=16, col=redgreen, tracecol="blue",
main="SpikeIn@pm Fold Changes\nrelative to 12.50 sample",
xlab="Relative Concentration", ylab="Probeset")
## End(Not run)
|
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