makeImap: Adds Interactive Information to 'Splot' Object

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

View source: R/makeImap.R

Description

The makeImap function will add all information needed to make a given figure in a Splot Object interactive. This function may be run more than once for a given figure.

Usage

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makeImap(Splot,
         figure=1,
         xy.type=NA,
         x.pos,
         y.pos,
         x.right.pos=NA, 
         y.bottom.pos=NA,
         spot.radius = 5,
         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,
         sep.chr=":",
         font.type="Helvetica",
         font.color="black", 
         font.size="12",     
         bg.color="#D6E3F6",
         fname.root="Splot",
         dir="./",
         automap.method="mode",
         bb.clr=NA,
         bb.cex=2,
         returnVl=TRUE,
         saveFlag=FALSE,
         saveName="Splot.RData",
         cleanDir=TRUE)

Arguments

Splot

An Object of the class Splot

figure

Indicates which plot figure data corresponds to; this matches the numeric indication in the layout matrix.

xy.type

Indication of how the xpos and ypos values should be treated. Current options are "points", "image.midpoints", "image.boundaries", "image.box", "circle", "rect", and "poly". See details or vignette.

x.pos

numeric vector of x values for interactive points. If xy.type is "rect", a numeric vector of the x.left position of rectangle[s].

y.pos

numeric vector of y values for interactive points. If xy.type is "rect", a numeric vector of the y.top position of rectangle[s]

x.right.pos

If xy.type is "rect", a numeric vector of the x.right position of rectangle[s]

y.bottom.pos

If xy.type is "rect", a numeric vector of the y.bottom position of rectangle[s]

spot.radius

radius of circle in pixels indicating area that will be interactive around the center of graphed points.used when xy.type is "points", "image.midpoints","image.boundaries", or "circle"

x.labels

data frame of n x m which contains values relating to the xpos. This information is displayed in the interactive plot window. See details or vignette

y.labels

data frame of n x m which contains values relating to the ypos. This information is displayed in the interactive plot window. See details or vignette

xy.labels

list of matricies. All matricies should be of n x m. This information is displayed in the interactive plot window. See details or vignette

x.links

data frame of n x m which contains web addresses for links relating to the xpos. This information is displayed as hyperlinks in the interactive plot window. See details or vignette

y.links

data frame of n x m which contains web addresses for links relating to the ypos. This information is displayed as hyperlinks in the interactive plot window. See details or vignette

xy.links

list of matricies. All matricies should be of n x m. This information is displayed in the interactive plot window as hyperlinks. The values in these matricies should be complete web address. See details or vignette

asLinks

contains complete web address for points that should be treated as hyperlinks. See details or vignette

x.images

data frame of n x m which contains paths to images relating to the xpos. n should be the length of the xpos argument if xy.type is "image.midpoints" and length of xpos - 1 if xy.type is "image.boundaries" or "image.box". m columns contains information regarding sample. This information is displayed as images in the interactive plot window.

y.images

data frame of n x m which contains paths to images relating to the ypos. n should be the length of the ypos argument if xy.type is "image.midpoints" and length of ypos - 1 if xy.type is "image.boundaries" or "image.box". m columns contains information regarding sample. This information is displayed as images in the interactive plot window.

xy.images

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 when xy.type is "image.midpoint". All matricies should be of n x m where n is the length of y -1 and m is the length of x - 1 when xy.type is "image.boundaries" or "image.box". This information is displayed in the interactive plot window as images. The values in these matricies should be complete paths to images

sep.chr

seperation character in tool tip that distinguishes value from indicator. If a single value, duplicated for all. It may be a vector of values corresponding to each tooltip entry.

font.type

font type for tool-tip. Currently support fonts are Arial, Helvetica,and sans-serif

font.color

font color for tool-tip

font.size

font size in tool-tip

bg.color

background color of tool-tip

fname.root

Base name to use for .png file name

dir

directory path to where files should be created

automap.method

Method to detect upper and lower bounds. Current options are "mode" or "median"

bb.clr

vector of possible color choices for automatic detection bound point. see details or vignette

bb.cex

Size of automatic detection bound point. see details or vignette

returnVl

Should Splot object be returned

saveFlag

Should Splot object be saved

saveName

If saveFlag, path file name to save object

cleanDir

logical indicating if the intermediate files generated by the application should be deleted. The files deleted are of no consequence to the user; they are needed to identify correct mapping

Details

Users are encouraged to see vignette for further details and several examples. Two of the most common reasons for automap failing to detect bounding points concerns the color of 'phantom' boundings points with the color of the graphs, and the figure regions/resize value. If the 'phantom' point color is the same as the color used in that area of the graph, a difference will not be recorded. The point color is determined by bb.clr. By default, if bb.clr is left as NA, we try the following colors: blue, red, black, white, green. If the size of the plotting region is small, and therefore the point size is small, or if the resize value is very large, the difference of color for a single point will not register. The point size does not equate to a pixel. In this case the user may try increasing the size of the 'phantom' points added through the bb.cex argument. xytype refers to how the x.pos and y.pos are treated. The possible options are "points", "image.midpoints", "image.boundaries", "image.box", "circle", "rect", and "poly". "Points","image.midpoints", and "circle" are handled the same. They assume the user is passing in x.pos and y.pos locations for a circle/point. image.midpoints is slightly different only in that it assumes the points refer to the center of regions in an image. The html image map will be a "circle". x.pos and y.pos will be the same length. "image.boundaries" assumes the x.pos and y.pos locations are referring to an image. The x.pos and y.pos locations are the boundaries of the regions, in other words, they are indications of x-axis and y-axis grid lines. The function will automatically calculate midpoints of the region and continues as if image.midpoints. "image.box" assumes x.pos and y.pos locations are referring to an image. The x.pos and y.pos locations are the boundaries of the regions,in other words, they are indications of x-axis and y-axis grid lines. The function calculates the boundaries of each rectangular image region to make interactive. The html image map will be a "rect". "rect" assumes the interactive regions are rectangular regions. x.pos refers to the left x coordinate[s] of the rectangular region[s]. y.pos refers to the top y coordinates[s] of the rectangular region[s]. When xy.type is "rect", x.right.pos and y.bottom.pos must also be specified indicating the right x and bottom y coordinate[s] respectively. x.pos, y.pos, x.right.pos, and y.bottom.pos will all be the same length. The html image map will be a "rect". "poly" assumes that one, and only one interactive polygon region is being added. The x.pos and y.pos therefore are the x and y vertices locations. The html image map will be a "poly". The dimensions of x.lables, y.labels, xy.labels, x.links, y.links, xy.links, and asLinks will depend on xy.type. If xy.type is "points","circle",or "rect" x.labels, y.lables, x.links, and y.links will have the dimensions n by m where n is equal to the length of x.pos. asLinks will also be of length x.pos, or a single value that will be repeated. xy.labels and xy.links will be a list of matricies where each matrix is also n by m where n is equal to the length of x.pos. If xy.type is "image.midpoints" the following is true. x.labels and x.links should be n by m where n is equal to the length of x.pos, just as y.lables and y.links will be of length y.pos. xy.lables and xy.links will be lists of n by m matricies where n is the length of y.pos and m is the length of x.pos. asLinks can be of length x.pos, y.pos, (x.pos*y.pos), or 1. If xy.type is "image.boundaries" or "image.box" are very similar to "image.midpoints". Instead of length x.pos and y.pos the length is x.pos-1 and y.pos-1. If xy.type is "poly", x.lables, y.lables, x.links, y.links, and the matricies in xy.lables and xy.links are all 1 by m. asLinks is a single values.

Value

If returnVl, returns updated Splot object. Also creates .png and .tif files used for automatic detection

Note

Automatic detection is currently only functional for linux/unix users. A windows extension is being worked on for future version. See details and vignette for notes on common reasons for automap failing.

Author(s)

Lori A.Shepherd, Daniel P. Gaile

References

Eric Kort (2006). rtiff: A tiff reader for R.. R package version 1.1.

See Also

initSplot,sendplot, makeSplot,rtiff

Examples

1
# Please see vignette or makeSplot for example

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