heatmap.send {sendplot}R Documentation

INTERACTIVE HEATMAP

Description

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.

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,
             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, '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 *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
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 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]
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 images in the interactive plot window. This may be left NA
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 left as NA
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. The values in these matricies should be complete path of images
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 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
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

Details

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.

Value

creates the static and interactive versions of heatmap

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.

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

Author(s)

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

References

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

See Also

initSplot,makeImap,makeSplot,imagesend,heatmap.send.legacy, sendplot, heatmap

Examples


library(sendplot)
library(rtiff)

require(graphics)

x  = as.matrix(mtcars)
rc = rainbow(nrow(x), start=0, end=.3)
cc = rainbow(ncol(x), start=0, end=.3)

xy.labels=list(value=x)

x.labels=data.frame(label=colnames(x),
  description=c("Miles/(US) gallon","Number of cylinders",
    "Displacement (cu.in.)",
    "Gross horsepower",
    "Rear axle ratio",
    "Weight (lb/1000)",
    "1/4 mile time",
    "V/S",
    "Transmission (0 = automatic, 1 = manual)",
    "Number of forward gears",
    "Number of carburetors")
  )

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

heatmap.send(x,scale="column", xy.labels = xy.labels,
                 x.labels=x.labels,
                 RowSideColors = rc, ColSideColors = cc, margin=c(5,10),
                 xlab = "specification variables", ylab= "Car Models",
                 main = "mtcars data",
                 fname.root="exHeat",dir=direct,
                 font.size=18,image.size="600x900")



[Package sendplot version 3.7.0 Index]