HeatmapWrapper: INTERACTIVE HEATMAP - DEPRECATED
In sendplot: Tool for sending interactive plots with tool-tip content.

Description Usage Arguments Details Value Note Author(s) References See Also Examples

This function is a wrapper for the R stats package heatmap. This will create an interactive heatmap image. NOTE: The majority of the code for this function is verbatim from the R package stats heatmap function. This function was designed to work as a wrapper to untilize the same functionality and plotting as the heatmap function with sendplot's interactive functionality.

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")

`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, 'NULL', see heatmap argument
`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 identically to the rows
`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 symmetrically; 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 left NA
`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 as hyperlinks in the interactive plot window. This may be left NA
`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 may be left as NA
`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. The values in these matricies should be complete web address
`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 of length equal to the first dimension of the x argument that will be repeated, a vector of length equal to the second dimension of the x argument that will be repeated,a non NA value of length 1 that will be repeated for all points, or a vector of length dim(x)[1]*dim(x)[2]
`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 output. Unix has a convert function that can convert a ps file to png file; we by default use this setup because we feel the postscript file maintains better quality. So on unix/linux systems if source.plot is NA, source.plot will be set to ps. Windows does not have this option, for this reason source.plot will be set to png if left NA
`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 application is kolourpaint and for windows it is microsoft paint (mspaint)
`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

The majority of the code for this function is verbatim from the R package stats heatmap function. This function was designed to work as a wrapper to untilize the same functionality and plotting as the heatmap function with sendplot's interactive functionality. See heatmap for more details on arguments and details concerning the creatation of plots.

See sendplot for more information regarding the creation of the interactive output with tool-tip content.

Users are encouraged to read the package vignette which includes a detailed discussion of all function arguments as well as several useful examples.

Creates a static .ps and .png file, and an interactive html file

The x and y mappings to the interactive plot are created using the x and y vectors passed in as an argument to sendplot. Note: this could be handy if for example the user plotted more points to the first plot using the plt.extras argument. If the user wanted all points interactive, the x and y values of the sendplot argument would be a combination of all plotted points.

The interactive html plot currently only works in web browsers that implement java script.

The code used to create the javascript embedded in html file is a modified version of the javascript code or from the open source tooltip library. see reference links

This function is deprecated. Please see heatmap.send for updated version.

Lori A. Shepherd and Daniel P. Gaile;

Authors of heatmap code used in our code: Andy Liaw, original; R. Gentleman, M. Maechler, W. Huber,revisions

http://www.R-project.org

http://www.onlamp.com/pub/a/onlamp/2007/07/05/writing-advanced-javascript.html

http://www.walterzorn.com/tooltip/tooltip\_e.htm

heatmap.send, sendplot,sendxy, sendimage, heatmap

rm(list=ls())
library(sendplot)

# mock matrix of values
temp = matrix(rnorm(15), nrow=5, ncol=3)

# color bars for samples
rcol = c("red", "blue", "yellow", "purple", "blue")
ccol = c("black", "green", "black")

# matrix of values to display in interactive window
temp.inv = list()
temp.inv$sample.ID = c("smp1", "smp2", "smp3")
temp.inv$count = 1:3
temp.inv$bb = 3:1
temp.inv = as.data.frame(temp.inv)

# matrix of values to display in interactive window
loc.inv = list()
loc.inv$spot = c("sp1", "sp2", "sp3","sp4","sp5")
loc.inv$vv = 1:5
loc.inv$bv = 5:1
loc.inv = as.data.frame(loc.inv)


#set up temporary directory
direct = paste(tempdir(),"/",sep="")
direct

heatmap.send.legacy(temp, RowSideColors=rcol, ColSideColors=ccol,
x.lbls=temp.inv, y.lbls=loc.inv, bound.pt=FALSE, paint=FALSE,
spot.radius=20, dir=direct)


# or display heatmap without color bands 
heatmap.send.legacy(temp, x.lbls=temp.inv, y.lbls=loc.inv, bound.pt=FALSE,
paint=FALSE, spot.radius=20,dir=direct)


# or without cluster
heatmap.send.legacy(temp, Rowv=NA, Colv=NA, x.lbls=temp.inv, y.lbls=loc.inv, bound.pt=FALSE,
paint=FALSE, spot.radius=20,dir=direct)