Lattice and trellis graphics (mostly splom)

CONT INTG DMNR DILG CFMG DECI PREP FAMI ORAL WRIT PHYS RTENAARONSON,L.H. 5.7 7.9 7.7 7.3 7.1 7.4 7.1 7.1 7.1 7.0 8.3 7.8ALEXANDER,J.M. 6.8 8.9 8.8 8.5 7.8 8.1 8.0 8.0 7.8 7.9 8.5 8.7ARMENTANO,A.J. 7.2 8.1 7.8 7.8 7.5 7.6 7.5 7.5 7.3 7.4 7.9 7.8BERDON,R.I. 6.8 8.8 8.5 8.8 8.3 8.5 8.7 8.7 8.4 8.5 8.8 8.7BRACKEN,J.J. 7.3 6.4 4.3 6.5 6.0 6.2 5.7 5.7 5.1 5.3 5.5 4.8BURNS,E.B. 6.2 8.8 8.7 8.5 7.9 8.0 8.1 8.0 8.0 8.0 8.6 8.6...

pairs(USJudgeRatings[1:5], panel=panel.smooth, cex = 1.5, pch = 24, bg="light blue", cex.labels = 2, font.labels=2, diag.panel=panel.hist, upper.panel=panel.cor)

But actual data often contains categorical (factor), continuous, temporal and censored variables

treat sex age height weight inherit steroids propylac hos.cat tstart enum tstop statusplacebo male 26 178.5 69.3 X-linked 0 1 US:other 0 1 203 0placebo male 9 129.4 28.7 X-linked 0 1 US:other 0 1 278 0placebo female 26 153.0 46.9 autosomal 0 1 US:NIH 0 1 306 0placebo male 27 176.0 82.8 autosomal 0 1 US:NIH 0 1 294 1

Test with the Chronic Granulotomous Disease data 2012-02-24

Analy st: John

Plotted: 2012-02-24 12:58:02 Data: dat (An 203x5 matrix)

-- Random sample of the input data --

sex treat inherit steroids OS160 male rIFN-g X-linked 0 277

32 male placebo X-linked 0 43 female rIFN-g autosomal 0 41

17 female rIFN-g autosomal 0 364104 male rIFN-g X-linked 0 38

sex

100

68

20

15

plcbplcb rIFNrIFN

mal

efe

ml

mal

efe

ml

126

42

5

30

X-lnX-ln atsmatsm

mal

efe

ml

mal

efe

ml

167

1

29

6

00 11

mal

efe

ml

mal

efe

ml

||||

| | || || | ||| || || ||| | |

||||| |||||||||||| | || | | ||||||| ||||||||||||||||||||||||||||||||||||||||||

f emalemale

treatsex

chisqp=0.9

treat

74

46

57

26

X-lnX-ln atsmatsm

plcb

rIF

Npl

cbrI

FN

114

6

82

1

00 11

plcb

rIF

Npl

cbrI

FN

||||||| ||||||| | ||| | |||| || |||||||||||||||||||||||| ||

||| |||| || | ||| | || | | |||||||||||||||||||||||||||||||||

|||

placeborIFN-g

inhert

sexchisq

p=3e-11

inherttreatchisqp=0.4

inherit

126

5

70

2

00 11

X-ln

atsm

X-ln

atsm

||||| |||| | || |||

|| ||||||||| |||| |||| |||

||| ||||||||||| | || | | | ||||| ||||||||||||||||||||||||||||||||||||||||||

autosomalX-linked

sterds

sex

chisqp=1e-05

sterdstreatchisqp=0.3

sterdsinhertchisqp=1

steroids

||||| |||||||||||| |||| ||| |||||||| || ||||||||||||||||||||||||||||||||||||||||||||||||||

|

|

|

01

OSsex

LogRankp=0.3

OS

treat

LogRank

p=1e-05

OSinhert

LogRankp=0.3

OSsterds

LogRankp=0.2

OS sex treat inherit steroids OS139 male placebo X-linked 0 2385 female placebo autosomal 0 33070 male rIFN-g X-linked 0 1160 male placebo X-linked 0 141164 male placebo autosomal 0 54100 male placebo X-linked 0 3498 male placebo X-linked 0 18172 male rIFN-g X-linked 0 304166 male rIFN-g X-linked 0 26361 male placebo X-linked 0 17541 male placebo X-linked 0 36113 male placebo X-linked 0 318161 male rIFN-g X-linked 0 25924 male placebo X-linked 0 19196 female rIFN-g autosomal 0 197127 male rIFN-g X-linked 0 29736 male rIFN-g autosomal 0 3294 male placebo X-linked 0 136 male placebo autosomal 0 12692 female rIFN-g autosomal 0 334174 female placebo autosomal 0 271201 female placebo autosomal 0 104188 male placebo autosomal 0 11124 male placebo autosomal 0 2286 male placebo X-linked 0 30049 male rIFN-g X-linked 0 360134 female rIFN-g autosomal 0 30344 male placebo X-linked 0 344184 male placebo X-linked 0 91107 female placebo X-linked 1 30

Etc. etc.

Example of my splom ‘supergraphic’

Splom – Scatter PLot Matrix

Multi-panel Conditioning

Test with the Chronic Granulotomous Disease data 2012-02-24

Analy st: John

Plotted: 2012-02-24 12:58:02 Data: dat (An 203x5 matrix)

-- Random sample of the input data --

sex treat inherit steroids OS160 male rIFN-g X-linked 0 277

32 male placebo X-linked 0 43 female rIFN-g autosomal 0 41

17 female rIFN-g autosomal 0 364104 male rIFN-g X-linked 0 38

sex

100

68

20

15

plcbplcb rIFNrIFN

ma

lefe

ml

ma

lefe

ml

126

42

5

30

X-lnX-ln atsmatsm

ma

lefe

ml

ma

lefe

ml

167

1

29

6

00 11m

ale

fem

lm

ale

fem

l||

||| | || || | ||| || || ||| | |

||||| |||||||||||| | || | | ||||||| ||||||||||||||||||||||||||||||||||||||||||

f emalemale

treat

sex

chisq

p=0.9

treat

74

46

57

26

X-lnX-ln atsmatsmpl

cbrI

FN

plcb

rIF

N

114

6

82

1

00 11

plcb

rIF

Npl

cbrI

FN

||||||| ||||||| | ||| | |||| || |||||||||||||||||||||||| ||

||| |||| || | ||| | || | | |||||||||||||||||||||||||||||||||

|||

placeborIFN-g

inhert

sexchisq

p=3e-11

inhert

treatchisq

p=0.4

inherit

126

5

70

2

00 11

X-ln

ats

mX

-lnat

sm

||||| |||| | || |||

|| ||||||||| |||| |||| |||

||| ||||||||||| | || | | | ||||| ||||||||||||||||||||||||||||||||||||||||||

autosomalX-linked

sterds

sex

chisqp=1e-05

sterds

treat

chisq

p=0.3

sterds

inhert

chisq

p=1

steroids

||||| |||||||||||| |||| ||| |||||||| || ||||||||||||||||||||||||||||||||||||||||||||||||||

|

|

|

01

OS

sex

LogRank

p=0.3

OS

treat

LogRank

p=1e-05

OS

inhert

LogRank

p=0.3

OS

sterds

LogRank

p=0.2

OS

Detail view of factor – factor and factor – censored panels

Shading proportional to the significance of the box

Raw counts in each box

Internal factor labels

Drop lines for events (also on the axes)

Example of the same data, but with violin plots vs. Q-Q plots to show two ways of depicting factor – continuous data

Information text and numbers

proportional to significance of the

results

A small sample of the

underlying data as part

of the sub-text

Same

Details of the call

splom(~dat, data=dat, par.settings=simpleTheme(col=brewer.pal(n=8, name="Dark2"), pch=19:25), auto.key=list(space="right"), main=paste("Test with the Chronic Granulotomous Disease data", Sys.Date()), sub=subText(data=dat, rot=0), xlab=NULL, alpha=0.3, varname.cex=0.6, axis.line.col="antiquewhite", axis.line.lty=3, pscales=0,

use.prefix=TRUE, digits=1, cex.cor=NULL, text.cex=0.6, factor.numeric="violin", guess=TRUE, prepanel.limits = guessDataLimits, lower.panel = panel.graphicSplom, upper.panel = panel.numericSplom)