sendplot (version 0.1.4)

sendPlot: CREATES WEB BROWSER INTERACTIVE PLOT

Description

This function takes in a layout, a list of plot calls, and sample information. It generates a static image of plots. It also generates an html file with an interactive version of the image.

Usage

sendplot(mat, plot.calls,  x,y, mai.mat=NA, xlim=NA, ylim=NA,
         z=NA,z.value="value", type="scatterplot", plt.extras =NA,
         x.lbls=NA, y.lbls=NA, xy.lbls=NA,
         bound.pt = TRUE,source.plot=NA,
         resize="4000x5500", ps.paper="letter",ps.width=8,
         ps.height=11,fname.root="test",dir="./",
         paint=TRUE, img.prog = NA,
         up.left=c(673,715),low.right=c(2874,4481),
         spot.radius=10)

Arguments

mat

matrix indicating layout. This argument will be passed into the graphics package layout call as mat.Each value in the matrix must be '0' or a positive integer. If N is the largest positive integer in the matrix, then the integers {1,...,N-1}

plot.calls

character vector containing plot calls

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

xlim

xlim values for the first plot call. This is required to set up intereactive plot for scatterplots. May be left NA. If this is NA and type is scatterplot the xlim will become the range of x values

ylim

ylim values for the first plot call. This is required to set up interactive plot for scatterplots.May be left NA. If this is NA and type is scatterplot the ylim will become the range of y values

x

vector of x values for the first plot call

y

vector of y values for the first plot call

z

vector of z values if the fist plot call is an image. If the plot call is not an image this may be left as NA

z.value

character vector indicating the label for what the z argument holds.

type

type of plot for the first plot call. Currently supports types are scatterplot or image

plt.extras

List of length equal to the number of plot.calls. This object is a list of lists. The sublists contain any additional plotting calls that should be executed for the plot. Each entry must be a character vector. If no additional plotting is

x.lbls

data frame of n x m which contatins values relating to the x axis of the first plot. n should be the length of the x argument. m columns contains information regarding sample. This information is displayed in the interactive plot window

y.lbls

data frame of n x m which contatins values relating to the y axis of the first plot. n should be the length of the y argument. m columns contains information regarding sample. This information is displayed in the interactive plot window

xy.lbls

list of matricies. All matricies should be of n x m where n is the length of y and m is the length of x. This information is displayed in the interactive plot window

bound.pt

logical indicating if red points should be plotted to aid in finding the upper left and lower right coordinates of a scatterplot. 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

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

Value

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

Details

This function allows the ability to create a static image of multiple plots. It also provides the functionality to make a plot interactive in a web browser utilizing javascript. This function utilizes the R graphics layout command and the package's eval.js command to make a collage of plots. The first plot in the plot.calls argument can be interactive in a web browser. The graphs currently supported are scatterplot and image which should be indicated by the argument type. The function uses information regarding x and y values to make a mapping that javascript can utilize. In order to map correctly, the x and y values need to be converted into pixel values. This is performed automatically, however it requires the knowledge of the upper left and lower right pixel coordinates of the bounding box of the first plot. These pixel coordinates change when the postscript file is converted into a .png file if the resize option is used. The .png file must be opened in some image viewer that allows the user to retrieve pixel coordinates. There are two possible scenerios for making a png file: the png file may be made directly, or a postscript file may be made first that then must be converted into a png file. We recommend the later because we feel it maintains better clarity and quality. Whether the ps or png file is made is controlled by source.plot. source.plot may be ps, png, or NA. If ps, the postscript file is created; if this option is chosen and the operating system is unix/linux there is an automatic call to the convert function to convert the postscript into a png file. If png, the .png file is created. If source.plot is NA, the operating system is checked and the appropriate file format is generated. By default, if the operating system is unix/linux, the postscript is created and then converted to png. If the operating system is windows or mac, the png file is created directly. If the ps option is used on windows or mac, it is up to the user to correctly convert the postscript to a png file format. As mentioned above, once the png file is created the pixil locations of the bounding box must be known. If paint is TRUE, the png file is openned with the program given by img.prog. If img.prog is NA, the application used to view the image is determined by the operating system. In windows,img.prog is mspaint which will open the .png file in microsoft paint. In linux/unix, img.prog is kolourpaint. img.prog may be any command line call to a graphics program for viewing .png files. The general plot call in R adds a buffer before the axis, for this reason we add two points at the bounding box. If bound.pt is T, two red points will appear in the scatterplot. When the file is opened in kolourpaint or mspaint, the user need only to record the pixel location when the mouse hovers over these red points (NOTE: in kolourpaint and mspaint the pixel location appears on the bottom of the window). If an image is desired as the main plot, the upper left and lower right corner of the image should be the points used. When the file is opened in kolourpaint or mspaint, the user need only to record the pixel location when the mouse hovers over these edges. If bound.pt is T, two blue points will appear in the image at these edges to aid in finding the location. When bound.pt is TRUE the function assumes that the user needs to find the pixel locations of the bounding box and will not make the html file. The interactive html file is only created when bound.pt is FALSE. Once the upper left and lower right values are recorded, the user should rerun the same function call but updating the up.left and low.right with the values retrieved and with bound.pt = FALSE. This results in an html with embedded javascript to be created. The user may open the html file in a web browser that has javascript capabilities; we recommended using mozilla firefox (NOTE: Internet Explorer currently does not support this function. Capability issues will be resolved in future releases). The information that appears when a point is scrolled over is controlled by the function arguments x.lbls, y.lbls, and xy.lbls. In a scatterplot x.lbls, y.lbls, and xy.lbls all refer to the same points. It is, therefore only necessary to specify x.lbls with information. In an image, there may be a differring number of x and y values. The information displayed can be from x specific information, y specific information, or information that is dependent upon both x and y. x.lbls is a data frame of x specific data. The number of rows should be equal to the number of x data points. There may be any number of columns. The names of the columns are used as the label in the display window. Likewise, y.lbls is a data frame of y specific data. The number of rows should be equal to the number of y data points. There may be any number of columns. The names of the columns are used as the label in the display window. xy.lbls however is a list of data frames. This data is dependent upon both x and y location. All data frames will be of the dimensions (length of y) X (length of x). There may be any number of data frames in the list. The name of the data frame, or the name in the list, is what is used as the label in the display window. The z value used to create the image is included automatically. Its label in the display window may be controlled by z.value. If this is not specified the default label is value.

References

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

See Also

layout, postscript, sendxy, sendimage

Examples

# see vignette for more advanced example


#
# first example of scatterplot
#
# note: we assume that the function has already been run once
#       to retrieve the pixel locations of the upper left and lower
#       right corners. If this had not been the case, the function would
#       need to have been run with bound.pt = T, perhaps paint = T
#       
#
# The up.left and low.right values are correct if run in 
#  unix/linux environment - for window users the coordinates will not be
#  correct


library(sendplot)

# create a layout with four plots
mat = matrix(c(rep(c(rep(3,8),rep(5,2)),1),
       rep(c(rep(1,8),rep(4,2)),14),
       rep(c(rep(2,8),rep(6,2)),2)),
       ncol=10,byrow=TRUE)

# create x and y points 
x=rnorm(16)
y=rnorm(16)

# list of plot calls - what plot call to use for the four plots
plot.calls = c("plot(x,y,col='green', pch=3)","plot(0,0, col='purple',pch=22,bg='purple')","plot(1:3,1:3, type='b',pch=21,bg='red',col='red')","curve(x^3-3*x,-2,2, col='blue')")

# create matrix of margin parameters
mai.mat = matrix(0, ncol=4, nrow=4, byrow=TRUE)
m1 = c(.25,0,.25,.5)
m2 = c(.4,0,.25,.5)
m3 = c(.1,0,.1,.5)
m4 = c(.25,0,.25,0)
mai.mat[1,] = m1
mai.mat[2,] = m2
mai.mat[3,] = m3
mai.mat[4,] = m4

# x and y limits of the first graph in the plot call
# in this case xlim and ylim values of plot(x,y,col='green', pch=3)
xlim = range(x, na.rm=TRUE)
xlim = c(xlim[1]-.1, xlim[2]+.1)
ylim = range(y, na.rm=TRUE)
ylim = c(ylim[1]-.1, ylim[2]+.1)

# data frame of sample information to display in interactive plot
# since scatterplot has equal number of pts no need to be x, y, or xy specific
x.lbls = list()
x.lbls$test = rep(c("a","b","c","d"),4)
x.lbls$num = 1:16
x.lbls = as.data.frame(x.lbls)





sendplot(mat, plot.calls, mai.mat,
         xlim=xlim, ylim=ylim,type="scatterplot",
         x=x,y=y,z=NA,
         x.lbls=x.lbls, y.lbls=NA, xy.lbls=NA, source.plot=NA,
         resize="1200x1700", fname.root="testScatterplot",dir="",
         paint=FALSE, bound.pt=FALSE,img.prog = NA,
         spot.radius=5, up.left=c(186,199),low.right=c(767,1264))

# there will now be a static postscript and .png file that may be viewed
# as well as an html file that can be opened with firefox that has
# interactive version 



#
#
# second example of image
#
# note: we assume that the function has already been run once
#       to retrieve the pixel locations of the upper left and lower
#       right corners. If this had not been the case, the function would
#       need to have been run with perhaps paint = T 
#       
#
# The up.left and low.right values are correct if run in 
#  unix/linux environment - for window users the coordinates will not be
#  correct


library(sendplot)

# create a layout with four plots
mat = matrix(c(rep(c(rep(3,8),rep(5,2)),1),
       rep(c(rep(1,8),rep(4,2)),14),
       rep(c(rep(2,8),rep(6,2)),2)),
       ncol=10,byrow=TRUE)

# create x and y points, and z matrix of values for image 
y=c(1:5,10,20,22,30,36) 
x=c(1,2,4,5,8)
z=matrix(rnorm(50), nrow=5, ncol=10)

# list of plot calls - what plot call to use for the four plots
plot.calls = c("image(x=x, y=y, z=z)",
    "plot(0,0, col='purple',pch=22,bg='purple')","plot(1:3,1:3, type='b',pch=21,bg='red',col='red')","curve(x^3-3*x,-2,2, col='blue')")

# create matrix of margin parameters
mai.mat = matrix(0, ncol=4, nrow=4, byrow=TRUE)
m1 = c(.25,0,.25,.5)
m2 = c(.4,0,.25,.5)
m3 = c(.1,0,.1,.5)
m4 = c(.25,0,.25,0)
mai.mat[1,] = m1
mai.mat[2,] = m2
mai.mat[3,] = m3
mai.mat[4,] = m4

# mock data frames of x specific and y specific data
x.lbls = list()
x.lbls$test = c("a","b","c","d","e")
x.lbls$num = 1:5
x.lbls = as.data.frame(x.lbls)
y.lbls = list()
y.lbls$test2 = rep(c("f","g","h","i","j"),2)
y.lbls$num2 = 10:1
y.lbls=as.data.frame(y.lbls)

# mock list of data frames of xy specific data
xy.lbls = list()
xy.lbls$one = matrix(1,nrow=10,ncol=5)
xy.lbls$two = matrix(2,nrow=10,ncol=5)
xy.lbls$aa = matrix("a", nrow=10,ncol=5)





sendplot(mat, plot.calls, mai.mat,
         xlim=NA, ylim=NA,type="image",
         x=x,y=y,z=z, z.value="value",
         x.lbls=x.lbls, y.lbls = y.lbls, xy.lbls=xy.lbls,
         resize="1200x1700", fname.root="testimage",source.plot=NA,
         dir="", paint=FALSE,img.prog = NA, bound.pt=FALSE, spot.radius=8,
         up.left=c(163,156),low.right=c(790,1310))


# there will now be a static postscript and .png file that may be viewed
# as well as an html file that can be opened with firefox that has
# interactive version