plotting: Plotting Functions

In kyotil: Utility Functions for Statistical Analysis Report Generation and Monte Carlo Studies

Plotting Functions

Description

mypostscript and mypdf sets the width and height based on mfrow input.

Usage

smoothed.scaled.hist (dat.ls, bin_width, scale.factors=NULL, cols=NULL, 
  legend=NULL, cex.legend=1, ...) 


myplot (object, ...) 

## S3 method for class 'loess'
myplot(object, xlab="x", ylab="fitted", ...)

whiskers (x, s, ...) 

abline.pt.slope(pt1, slope, x2=NULL, ...)

abline.pts(pt1, pt2 = NULL)

butterfly.plot(dat, dat2 = NULL, add = FALSE, xaxislabels = rep("", 4), x.ori = 0, 
    xlab = "", ylab = "", cex.axis = 1, ...)

empty.plot()

add.mtext.label (text, cex = 1.4, adj = -0.2) 
mydev.off(file = "temp", ext = c("pdf"), res = 200, mydev =
                 NULL, silent = TRUE)
getMfrow(len)

myhist (x, add.norm=TRUE, col.norm="blue", ...)

myforestplot(dat, xlim = NULL, xlab = "", main = "", col.1 = "red",
 col.2 = "blue", plot.labels = TRUE, order = FALSE,
 decreasing = FALSE, vline = TRUE, cols = NULL, log =
 "", null.val = NULL)

my.interaction.plot(dat, x.ori = 0, xaxislabels = rep("", 2), cex.axis = 1, add = FALSE,
    xlab = "", ylab = "", pcol = NULL, lcol = NULL, ...)

myboxplot(object, ...)

## S3 method for class 'formula'
myboxplot(formula, data, cex = 0.5, xlab = "", ylab = NULL, main
                 = "", box = TRUE, at = NULL, na.action = NULL, p.val =
                 NULL, pch = 1, col = "white", col.points = 1, border =
                 1, test = "", friedman.test.formula = NULL,
                 reshape.formula = NULL, reshape.id = NULL, jitter =
                 TRUE, add.interaction = FALSE, drop.unused.levels =
                 TRUE, bg.pt = NULL, add = FALSE, seed = 1,
                 write.p.at.top = FALSE, ...)
    
## S3 method for class 'data.frame'
myboxplot(object, cex = 0.5, ylab = "", xlab = "", main = "",
 box = TRUE, at = NULL, pch = 1, col = 1, test = "",
 paired = FALSE, ...)

## S3 method for class 'list'
myboxplot(object, paired = FALSE, ...)

abline.shade.2(x, col=c(0,1,0))
abline.shade(pt, type = 5, col = c(0, 1, 0), alpha = 0.3)


mylegend(legend, x, y=NULL, lty = NULL, bty = "n", ...)

mymatplot(x, y, type = "b", lty = c(1, 2, 1, 2, 1, 2), pch =
                 NULL, col = rep(c("darkgray", "black"), each = 3),
                 xlab = NULL, ylab = "", draw.x.axis = TRUE, bg = NA,
                 lwd = 1, at = NULL, make.legend = TRUE, legend = NULL,
                 impute.missing.for.line = TRUE, legend.x = 9,
                 legend.title = NULL, legend.cex = 1, legend.lty = lty,
                 legend.inset = 0, xaxt = "s", y.intersp = 1.5,
                 x.intersp = 0.3, text.width = NULL, add = FALSE, ...
)
                          
mypairs(dat, ladder = FALSE, show.data.cloud = TRUE,
 ladder.add.line = T, ladder.add.text = T, ...)

wtd.hist (x, breaks = "Sturges", freq = NULL, probability = !freq, 
    include.lowest = TRUE, right = TRUE, density = NULL, angle = 45, 
    col = NULL, border = NULL, main = paste("Histogram of", xname), 
    xlim = range(breaks), ylim = NULL, xlab = xname, ylab, axes = TRUE, 
    plot = TRUE, labels = FALSE, nclass = NULL, weight = NULL, 
    ...) 

mylines(x, y, type = "l", ...)

myfigure(mfrow = c(1, 1), mfcol = NULL, width = NULL, 
    height = NULL, oma = NULL, mar = NULL, main.outer = FALSE, bg=NULL) 


mypdf(...)

mypng(...)
mytiff(...)

mypostscript(file = "temp", mfrow = c(1, 1), mfcol = NULL, width =
                 NULL, height = NULL, ext = c("eps", "pdf", "png",
                 "tiff"), oma = NULL, mar = NULL, main.outer = FALSE,
                 save2file = TRUE, res = 200, silent = TRUE, ...)

panel.cor(x, y, digits = 2, prefix = "", cex.cor, cor., leading0
 = FALSE, cex.cor.dep = TRUE, ...)

panel.hist(x, ...)

panel.nothing(x, ...)

corplot(object, ...)

## Default S3 method:
corplot(object, y, ...)

## S3 method for class 'formula'
corplot(formula, data, main = "", method = c("pearson",
                 "spearman"), col = 1, cex = 0.5, add.diagonal.line =
                 TRUE, add.lm.fit = FALSE, add.loess.fit = FALSE,
                 col.lm = 2, add.deming.fit = FALSE, col.deming = 4,
                 add = FALSE, digit.cor = 2, log = "", same.xylim =
                 FALSE, xlim = NULL, ylim = NULL, ...)

Arguments

digit.cor	number of digits to print correlation
col.points	color of points
dat.ls	named list of vectors. A histogram is made for each vector.
bin_width	width of bin for histograms
scale.factors	named vector of scale factors to scale the histogram counts by
cex.legend	cex for legend
silent	tbdadd
legend.lty	tbdadd
cex.cor.dep	tbdadd
add.loess.fit	tbdadd
leading0	tbdadd
null.val	tbdadd
write.p.at.top	tbdadd
text.width	tbdadd
text	tbdadd
cex	tbdcex
adj	tbdpt2
file	tbdfile
ext	tbdext
res	resolution.
add.norm	Boolean, whether to add normal approximation density line
col.norm	string, color of added normal density line
pt1	tbdpt1
s	tbdslope
ladder	tbdslope
slope	tbdslope
friedman.test.formula	tbdslope
reshape.id	tbdslope
impute.missing.for.line	tbdslope
cor.	tbdslope
mydev	tbdslope
jitter	Boolean
add.interaction	Boolean
...	tbd...
xaxt	tbdpt2
breaks	tbdpt2
freq	tbdpt2
bg.pt	tbdpt2
probability	tbdpt2
include.lowest	tbdpt2
right	tbdpt2
density	tbdpt2
angle	tbdpt2
border	tbdpt2
axes	tbdpt2
plot	tbdpt2
labels	tbdpt2
nclass	tbdpt2
weight	tbdpt2
pt2	tbdpt2
pt	tbdpt2
alpha	tbdpt2
dat	tbddat
lwd	line width.
x.intersp	controls the look of legend.
y.intersp	controls the look of legend.
legend.inset	legend inset
dat2	tbddat2
add	tbdadd
log	log
add.lm.fit	lm fit
add.deming.fit	add
col.lm	col
col.deming	col
reshape.formula	a formula object.
xaxislabels	tbdxaxislabels
x.ori	tbdx.ori
xlab	tbdxlab
ylab	tbdylab
cex.axis	tbdcex.axis
len	tbdlen
same.xylim	Boolean. Whether xlim and ylim should be the same
xlim	tbdxlim
ylim	tbdxlim
main	tbdmain
col.1	tbdcol.1
col.2	tbdcol.2
pcol	tbdpcol
lcol	tbdlcol
object	tbdobject
formula	tbdformula
data	tbddata
box	tbdbox
at	tbdat
pch	tbdpch
col	tbdcol
test	string. For example, "t","w","f","k", "tw"
legend	tbdlegend
x	tbdx
lty	tbdlty
bty	tbdbty
type	tbdtype
make.legend	tbdmake.legend
legend.x	tbdlegend.x
legend.title	tbdlegend.title
legend.cex	tbdlegend.cex
draw.x.axis	tbddraw.x.axis
bg	tbdbg
method	tbdmethod
mfrow	tbdmfrow
mfcol	tbdmfcol
width	tbdwidth
height	tbdheight
oma	tbdoma
mar	tbdmar
main.outer	tbdmain.outer
save2file	tbdsave2file
y	tbdy
digits	tbddigits
prefix	tbdprefix
cex.cor	cex cor
plot.labels	Boolean
order	Boolean
decreasing	Boolean
add.diagonal.line	tbdadd.diagonal.line
x2	tbdadd.diagonal.line
vline	tbdadd.diagonal.line
cols	tbdadd.diagonal.line
na.action	tbdadd.diagonal.line
drop.unused.levels	tbdadd.diagonal.line
p.val	tbdx
seed	tbdx
paired	tbdx
show.data.cloud	tbdx
ladder.add.line	tbdx
ladder.add.text	tbdx

Details

myboxplot shows data points along with boxes. The data poins are jittered and the pattern of jittering is made reproducible in repeated calls. The test can only take one type of test currently.

myforestplot is modified from code from Allan deCamp/SCHARP. dat should have three columns. first column should be point estimate, second and third lci and uci, fourth p value. col.1 is the color used for CIs that do not include null, col.2 is used for CIs that do include null. If order is TRUE, the rows are ordered by the first column of dat. descreasing can be used to change the behavior of order.

corplot.formula uses MethComp::Deming by Bendix Carstensen to fit Deming regression.

wtd.hist is copied from weights package, author: Josh Pasek.

mymatplot will use na.approx (zoo) to fill in NA before plotting in order to draw continuous lines. The filled-in values will not be shown as points.

smoothed.scaled.hist draws histograms and overlay densities on top.

Examples

set.seed(1)
x=1:50+rnorm(50,0,4)
y=1:50+rnorm(50,0,4)
dat=data.frame(x, y)
corplot(y~x,dat,add.lm.fit=TRUE,add.deming.fit=TRUE,col.lm="red",col.deming="blue")

dat=data.frame(y=c(1:10,2:11), x=rep(c("a","b"),each=10), ptid=c(1:10,1:10))
par(mfrow=c(1,2))
myboxplot(y~x, dat, test="w", jitter=FALSE)
myboxplot(y~x, dat, test="f", add.interaction=TRUE, reshape.formula=y~x, reshape.id="ptid")


myboxplot(list(jitter(1:10), jitter(3:12)), test="w")
myboxplot(list(jitter(1:10), jitter(3:12)), test="w", paired=TRUE)

smoothed.scaled.hist(list(A=rnorm(100,0,1)), bin_width=0.1, xlab="x")
smoothed.scaled.hist(list(A=rnorm(100,0,1), B=rnorm(500,10,2)), 
                  bin_width=0.1, xlab="x")



## Not run: 
myfigure(mfrow=c(1,2))
    plot(1:10)
    plot(1:10)
mydev.off(ext="png,pdf", file="tmp")

## End(Not run)



#myboxplot x axis may look weird if log="xy"

kyotil documentation built on Nov. 3, 2024, 9:08 a.m.