Usage
heatmap.send.legacy(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,
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"),
mai.mat=NA, mai.prc=FALSE,
z.value="value",
x.lbls=NA,y.lbls=NA,xy.lbls=NA,
x.links=NA, y.links=NA,
xy.links=NA,asLinks=NA,
bound.pt = FALSE, source.plot=NA,
resize="800x1100",
ps.paper="letter",ps.width=8,ps.height=11,
fname.root="test",dir="./", header="v2",
paint=FALSE, img.prog = NA,
up.left=c(288,203),low.right=c(620,940),
spot.radius=5, automap=FALSE, automap.method="mode")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'
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
mai.mat
n x 4 matrix of values to be passed in for each plots
par mai. n is equal to the length of plot.calls. If NA, uses default
margins. Utitilzing this wrapper n will either be 3,4, or 5.
mai.prc
logical indicating if mai mat values are percentages
or hard coded values. If mai.proc is T, indicates percentage.
z.value
character vector indicating the label for what the z
argument holds.
x.lbls
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.lbls
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.lbls
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
bound.pt
logical indicating if blue points should be plotted to
aid in finding the upper left and lower right coordinates of a
hte heatmap. If bound.pt is FALSE, indicates that up.left and
low.right arguments are correct and will make the html file
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
resize
character indicating resize value. The postscript
version will be resized to this value when converted to .png.
ps.paper
postscript paper argument
ps.width
poscript width argument
ps.height
postscript height argument
fname.root
Base name to use for posctscript, .png, and html
file names.
dir
directory path to where files should be created. Default
creates files in working directory
header
May either be v1 or v2. 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.
paint
logical indicating if application should
automatically open .png file for the user to view .png file and/or
to retrieve needed bounding values of the first plot call. see
details
img.prog
If paint is TRUE, the command line call that will open
a program to view .png file to retrieve pixil locations of interactive
plot bounds. If this is left NA, the operating system is checked and
a default program is used. For unix the default
up.left
The x and y value in pixels of the upper left hand
corner of the first plot call. see details
low.right
The x and y value in pixels of the lower right hand
corner of the first plot call. see details
spot.radius
radius of circle in pixels indicating area that
will be interactive around the center of graphed points
automap
automatic detection of up.left and low.right bound
points. Fully functional on linux/unix machines only.
automap.method
Method to detect upper and lower bounds. Current
options are mode or median