HeatmapWrapper: INTERACTIVE HEATMAP - DEPRECATED

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

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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
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, '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

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

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

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 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.

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

heatmap.send, sendplot,sendxy, sendimage, heatmap

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
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)

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