Usage
heatmap.send(x,Rowv = NULL,
Colv = if (symm) "Rowv" else NULL,
distfun = dist,hclustfun = hclust,
reorderfun = function(d,w) reorder(d, w),
add.expr,symm = FALSE,
revC = identical(Colv,"Rowv"),
scale = c("row", "column", "none"),
na.rm = TRUE, margins = c(5, 5),
ColSideColors,RowSideColors,
MainColor = heat.colors(12),
cexRow = 0.2 + 1/log10(nr),
cexCol = 0.2 + 1/log10(nc),
labRow = NULL,labCol = NULL,
main = NULL,xlab = NULL,ylab = NULL,
keep.dendro = FALSE,
verbose = getOption("verbose"),
x.labels=NA,y.labels=NA,xy.labels=NA,
x.links=NA, y.links=NA,
xy.links=NA,asLinks=NA,
x.images=NA, y.images=NA,
xy.images=NA,
spot.radius=5,source.plot=NA,
image.size="800x1100",
fname.root="test",dir="./", header="v3",
window.size = "800x1100",
...)Arguments
x
numeric matrix of the values to be plotted
Rowv
determines if and how the row dendrogram should be computed
and reordered. Either a 'dendrogram' or a vector of values
used to reorder the row dendrogram or 'NA' to suppress any
row dendrogram (and reordering) or by default,
Colv
determines if and how the column dendrogram should be
reordered. Has the same options as the 'Rowv' argument above
and additionally when 'x' is a square matrix, 'Colv =
"Rowv"' means that columns should be treated identicall
distfun
function used to compute the distance (dissimilarity) between
both rows and columns. Defaults to 'dist'
hclustfun
function used to compute the hierarchical clustering when
'Rowv' or 'Colv' are not dendrograms. Defaults to 'hclust'
reorderfun
function(d,w) of dendrogram and weights for reordering the
row and column dendrograms. The default uses
'reorder.dendrogram'
add.expr
expression that will be evaluated after the call to 'image'.
Can be used to add components to the plot
symm
logical indicating if 'x' should be treated *symm*etrically;
can only be true when 'x' is a square matrix.
revC
logical indicating if the column order should be 'rev'ersed
for plotting, such that e.g., for the symmetric case, the
symmetry axis is as usual
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"' if 'symm' false, and
'"none"' otherwise
na.rm
logical indicating whether 'NA''s should be removed
margins
numeric vector of length 2 containing the margins (see
'par(mar= *)') for column and row names, respectively
ColSideColors
(optional) character vector of length 'ncol(x)'
containing the color names for a horizontal side bar that may
be used to annotate the columns of 'x'
RowSideColors
(optional) character vector of length 'nrow(x)'
containing the color names for a vertical side bar that may
be used to annotate the rows of 'x'
MainColor
color scale for values. Passed into 'image' function
as col argument
cexRow
positive number, used as 'cex.axis' in for the row axis
labeling. The defaults currently only use number of rows
cexCol
positive number, used as 'cex.axis' in for the column axis
labeling. The defaults currently only use number of columns
labRow
character vectors with row labels to use;
these default to 'rownames(x)'
labCol
character vectors with column labels to use;
these default to 'colnames(x)'
main
main title; defaults to none
xlab
x axis title; defaults to none
ylab
y axis title; defautls to none
keep.dendro
logical indicating if the dendrogram(s) should be kept as
part of the result (when 'Rowv' and/or 'Colv' are not NA)
verbose
logical indicating if information should be printed
x.labels
data frame of n x m which contains values relating to the x
axis of the heatmap plot. n should be equal to the second dimension of the x
argument.This information is displayed in the interactive plot
window. This may be left as NA.
y.labels
data frame of n x m which contains values relating to the y
axis of the heatmap plot. n should be equal to the first dimension of the x
argument.This information is displayed in the interactive plot
window. This may be left as NA
xy.labels
list of matricies. All matricies should be of n x m
where n is equal to the first dimension of the x argument and m is
equal to the second dimension of the x argument. This information is
displayed in the interactive plot window. This may be l
x.links
data frame of n x m which contains web addresses
for links relating to the x axis of the heatmap plot. n should be
equal to the second dimension of the x argument. m columns contains
information regarding sample. This information is displayed
y.links
data frame of n x m which contains web addresses
for links relating to the y axis of the heatmap plot. n should be
equal to the first dimension of the x argument. This information is
displayed as hyperlinks in the interactive plot window. This
xy.links
list of matricies. All matricies should be of n x m
where n is equal to the first dimension of the x argument and m is
equal to the second dimension of the x argument. This information is
displayed in the interactive plot window as hyperlinks
asLinks
contains complete web address for points that should be
treated as hyperlinks. May be a data.frame or matrix of n x m where
n is equal to the first dimension of the x argument and m is equal
to the second dimension of the x argument, a vector
x.images
data frame of n x m which contains paths for images
relating to the x axis of the heatmap plot. n should be
equal to the second dimension of the x argument. m columns contains
information regarding sample. This information is displayed as
y.images
data frame of n x m which contains paths for images
relating to the y axis of the heatmap plot. n should be
equal to the first dimension of the x argument. This information is
displayed as images in the interactive plot window. This may be
xy.images
list of matricies. All matricies should be of n x m
where n is equal to the first dimension of the x argument and m is
equal to the second dimension of the x argument. This information is
displayed in the interactive plot window as images. Th
spot.radius
radius of circle in pixels indicating area that
will be interactive around the center of graphed points
source.plot
Indicates whether application should make a
postscript file and then convert to png file, or if the png file
should be made directly. This value is either ps, png, or NA. If NA
the operating system is checked and the appropraite file format is
image.size
character indicating size of device.
fname.root
Base name to use for all files created.
dir
directory path to where files should be created. Default
creates files in working directory
header
May either be v1,v2, or v3. This determines which
tooltip header will be in the html file. Each version has different
features or works well with different web browsers. see sp.header
for details.
window.size
size of the html window. Only effective when header=v3
...
additional arguments to the makeImap function