r graphics using the grid package sigal blay statistical genetics working group dept. of statistics...

R Graphicsusing the

Grid Package

Sigal BlayStatistical Genetics Working Group

Dept. Of Statistics and Actuarial ScienceSimon Fraser University

January 2006

Grid Low level graphics system Produces editable graphical components

(not just graphics output) Object Oriented - graphical components

can be reused and recombined

A standard set of graphical primitives:

grid.rect(...) grid.lines(...) grid.polygon(...)grid.circle(...)grid.text(...)

library(help = grid) for details

text

0 0.25 0.5 0.75 1

For every function of the form grid.* there is anequivalent function *Grob that returns a graphical objectbut doesn't draw it on the graphics device:grid.rect(...) rectGrob(...)grid.lines(...) linesGrob(...)grid.polygon(...) polygonGrob(...)grid.circle(...) circleGrob(...)grid.text(...) textGrob(..)

Usage:Rect <- rectGrob(...) grid.draw(Rect)

Graphical output can be positioned and sized

relative to a large number of coordinate systems

grid.rect(x = unit(0, “native"), y = unit(1.5, “npc"), height = unit(0.5, "inches"), width = unit(0.8, “lines”))

help(unit) for details

Can specify various graphical parametersgrid.rect(gp=gpar(col="red", lwd=2,

fill="yellow", lty="dotted"))grid.text(gp=gpar(col="red", fontsize=10,

fontface="italic"))

help(gpar)for details

text

0 0.25 0.5 0.75 1

Working with viewportsAll drawing occurs in the current grid viewport,a defined rectangular region with it's own definedcoordinate system:vp <- viewport(width=0.5, height=0.2, angle=45)

grid.show.viewport(vp)

help(viewport)for details 0.5npc

0.5n

pc

vp <- viewport(width=0.5, height=0.2, angle=45, name="VP")pushViewport(vp)grid.rect()popViewport()

vp <- viewport(width=0.5, height=0.2, angle=45, name="VP")pushViewport(vp)grid.rect() grid.xaxis()grid.yaxis()

00.

20.

40.

60.

81

00.2

0.6

1

vp <- viewport(width=0.5, height=0.2, angle=45, name="VP")pushViewport(vp)grid.rect()grid.xaxis()grid.yaxis()grid.text("viewport region", y = 0.9)

00.

20.

40.

60.

81

00.2

0.6

1vie

wport

regio

n

vp <- viewport(width=0.5, height=0.2, angle=45, name="VP")pushViewport(vp)grid.rect()grid.xaxis()grid.yaxis()grid.text("viewport region", y = 0.9)upViewport()grid.text("root region",y = 0.1)

00.

20.

40.

60.

81

00.2

0.6

1vie

wport

regio

n

root region

vp <- viewport(width=0.5, height=0.2, angle=45, name="VP")pushViewport(vp)grid.rect()grid.xaxis()grid.yaxis()grid.text("viewport region", y = 0.9)upViewport()grid.text("root region",y = 0.1)grid.text("more text", vp="VP“ y=0.7) 0

0.2

0.4

0.6

0.8

1

00.2

0.6

1vie

wport

regio

n

root region

mor

e te

xt

Query the viewport tree

> current.viewport()viewport[ROOT] > current.vpTree()viewport[ROOT]->(viewport[VP]) > downViewport("VP")> popViewport()> current.vpTree()viewport[ROOT]

Can push multiple viewport

pushViewport(vpList(vp1, vp2, vp3))

Can push nested viewports pushViewport(vpStack(vp1, vp2, vp3)) pushViewport(vpTree(vp1, vpList(vp2, vp3)))

Can integrate with a layout

plotViewport(...)a convenience function for producing a viewport

with a central plot region surrounded by margins given in terms of a number of lines of text.

dataViewport(...)a convenience function for producing a viewport

with x- and/or y-scales based on numeric values passed to the function.

grid creates graphical objects (grobs):

grid.rect(..., name="box")grid.circle(...)grid.edit("box", gp=gpar(fill="yellow"))grid.remove("box")

gTree – a tree of grobsvp<-viewport(..., name="view")x <- xaxisGrob(name = "axis1")y <- yaxisGrob(name = "axis2")points <- pointsGrob(1:9, 1:9,

name="dataPoints")title <- textGrob(..., name="myTitle")

tree <- gTree(name="Tree”, vp=vp, children=gList(x,y,title,points))grid.draw(tree)

0 2 4 6 8 10

0

2

4

6

8

10gTree - a tree of

graphical objects

Query and edit a gTree> getNames() # list all top-level grobs[1] "Tree“

> childNames(tree)[1] "axis1" "axis2" "myTitle“ "dataPoints"> childNames(grid.get("Tree"))[1] "axis1" "axis2" "myTitle“ "dataPoints"

> grid.add("Tree", grid.rect())> grid.edit(gPath("Tree","dataPoints"), pch=2)

0 2 4 6 8 10

0

2

4

6

8

10gTree - a tree of

graphical objects

Pairwise LD

Physical Length:8.9kb

*

*

rs2283092

rs6979287

Color Key

0 0.2 0.4 0.6 0.8 1

Example:LDheatmap package

Plots measures of pairwise linkage disequilibria for SNPs

> getNames()[1] "ldheatmap"

> childNames(grid.get("ldheatmap"))[1] "heatMap" "geneMap" "Key“

> childNames(grid.get("heatMap"))[1] "heatmap" "title"

> childNames(grid.get("geneMap"))[1] "diagonal" "segments" "title" "symbols“ "SNPnames"

> childNames(grid.get("Key"))[1] "colorKey" "title" "labels" "ticks” "box"

Pairwise LD

Physical Length:8.9kb

*

*

rs2283092

rs6979287

Color Key

0 0.2 0.4 0.6 0.8 1

grid.edit("symbols", pch=20, gp=gpar(cex=2))grid.edit(gPath("ldheatmap","heatMap","title"),

gp=gpar(col="red"))grid.edit(gPath("ldheatmap","heatMap","heatmap“), gp=gpar(col="white", lwd=2))

Pairwise LD

Physical Length:8.9kb

*

*

rs2283092

rs6979287

Color Key

0 0.2 0.4 0.6 0.8 1

Pairwise LD

Physical Length:8.9kb

rs2283092

rs6979287

Color Key

0 0.2 0.4 0.6 0.8 1

Conclusion

the R grid package

enables the production of

reusable and flexiblegraphical components

Further reading

R Graphics / Paul Murrell