heatmap.send: INTERACTIVE HEATMAP

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

View source: R/heatmap.send.R

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

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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, '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'

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 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

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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")

lshep/sendplot documentation built on Nov. 18, 2017, 5:10 p.m.