plotting {kyotil}

Plotting Functions

Description

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

Usage

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 = "", main =
 "", box = TRUE, at = NULL, na.action = NULL, p.val =
 NULL, pch = 1, col = 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, log = "", same.xylim = FALSE, xlim =
 NULL, ylim = NULL, ...)

Arguments

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.

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)

## 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"