battleship: Battleship plot

In vonthein/illustrator: Symbol Plots

Description

Battleship plot

Usage

battleship(y, cens = 0, x = 1, dis = "normal", xprop = T, space = 1,
  his = NA, binz = 0, err = F, loc = "none", prec = "2sd",
  connect = F, box = F, vio = F, dot = NA, icon = "loop",
  fill = FALSE, ship = T, plank = 2, dtr = F,
  fillcol = shape::shadepalette(length(unique(x)), "lightblue", IMBSgreen.),
  elicol = shape::shadepalette(length(unique(x)), "blue", "darkgreen"),
  errcol = shape::shadepalette(length(unique(x)), IMBSorange, "brown"),
  concol = shape::shadepalette(length(as.matrix(connect)[1, ]), IMBSorange,
  "brown"), hiscol = shape::shadepalette(length(unique(x)), "darkgreen",
  "darkblue"), boxcol = shape::shadepalette(length(unique(x)), "brown",
  IMBSorange), viocol = shape::shadepalette(length(unique(x)), IMBSorange,
  "brown"), shipcol = shape::shadepalette(length(unique(x)), IMBSorange,
  "brown"), quant = c(0.025, 0.25, 0.5, 0.75, 0.975), cline = FALSE,
  clc = "white", whisker = 0, confluence = "Tufte", trials = 0,
  start = list(m), mix = NA, genmix = F, df = 4, kern = "gaussian",
  sdsk = sqrt(var(y))/log(length(y)), ...)

Arguments

y	vector containing dependent variable
cens	vector of length(y), is > 0 where y is right-censored, is < 0 where left-censored, 0 elsewhere implemented for dist "lognormal", "normal", "gamma" or "weibull"
x	factor, same length as y
dis	distribution, "lognormal", "normal", "2normal", "t", "beta","gamma", "weibull","mixnorm", "poisson", "binomial", "betabinomial"
xprop	x-axis proportional to group sizes (joint distribution)? recommended, if dot=TRUE
space	multiplicative spacing in x-direction
his	plot histogram or probability function?
binz	numbers of bins for dotplots and histograms
err	draw error bar? Not drawn when data are censored
loc	location of error bar or error bars, if vector: "mean", "geomean"
prec	whiskers of error bar, "se", "sd", "2se", "2sd", applied to logarithms, if loc="geomean".
connect	whether arithmetic or geometric means according to loc are connected, as scalar logical value or matrix of integers <= number of x levels with one column per polygon
box	draw boxplots?
vio	draw something like a violin plot?
dot	plot dotplot? logical vector of length 1 or number of groups
icon	either a character name of predefined icons or a matrix with coordinates, when character vector or list of matrices of length = levels of x, then icon by x, when list of length = levels of x of character vectors of number of ys per level, or list of lists of matrices then single icons sorted first by x second by y
fill	fill icons? If sum(abs(cens)) > 0, then censored values are empty, others filled
ship	plot battleship? logical vector of length 1 or number of x levels
plank	line width for plotting ships and quantiles, if vector then for each ship
dtr	density trace residual?
fillcol	color the icons are filled with, when scalar then all the same, when vector of length = levels of x, then color by x, when list of length = levels of x of vectors of number of icons per level, color of single icons sorted first by x second by y
elicol	color the icons are bordered with, similar to fillcol
errcol	color the error bars are drawn in, similar to boxcol
concol	color the connecting lines are drawn in, similar to boxcol
hiscol	histogram color, if vector then for each histogram
boxcol	boxplot color, if vector then for each boxplot
viocol	violin color, if vector then for each violin
shipcol	ship color, if vector then for each ship
quant	vector of quantile for which bars are drawn across
cline	plot line(s) through the middle at x label?
clc	color(s) of line(s) through the middle
whisker	battleships are drawn to the whisker quantile, default = 0.5 / n_i
confluence	"Tukey" outlined bars, "Tufte" thin bars, "Duerr" circles
trials	size parameter of binomial distribution(s)
start	list of starting values for mixture parameters
mix	number of normals in a mixture
genmix	whether mixtures differ in proportions only
df	degrees of freedom of t-distribution(s)
kern	kernel of density trace for dtr or violin
sdsk	smoothness parameter of density trace for dtr or violin
...	parameters passed on to function plot()

Value

Prints tuning parameters binz and space and returns histograms of y for values of x. Plots the specified plot.

Examples

## Not run: 
x <- rep(c(1:4),c(100,100,100,100)*.1); y <- x+rnorm(40,x/2)
 battleship(y=y,x=x,dtr=FALSE,fill=TRUE,xprop=FALSE,
            ship=TRUE, dis="normal", plank=1, cline=TRUE,
            space=1.7, dot=TRUE, binz=13, icon=rabbit,
            fillcol=c("brown","gold","lightgray","white"))

# Aesthetic Symbol
# requires binz according to format
x <- rep(c(1:6),c(50,50,50,50,50,50)*2);y <- rep((rnorm(100)),6)
battleship(y=y,cens=0,x=x,binz=40,dtr=c(F,F,F,F,F,T),fill=T,xprop=F,
           space=2.2,dis="normal",plank=0.5,
           cline=c(F,T,F,F,F,F),clc="white",
           box=c(F,T,F,F,F,F),
           boxcol="black",
           dot=c(T,T,T,F,T,F),icon="arabidopsis",# fast quadratisch
           err=c(T,F,F,F,F,T),loc="mean",prec="2se",
           errcol=c("black","red","orange","white","blue","brown"),
           his=c(F,F,F,T,F,F),hiscol="darkgreen",
           vio=c(F,F,T,F,F,F),#viocol="green",
           ship=c(F,F,F,T,T,T),connect=matrix(c(1,2,5,6),2,2,F))

x <- rep(c(1:2),c(150,50)*.6); y <- x+rnorm(80,x/2)
battleship(y=y,x=x,dtr=FALSE,fill=TRUE,xprop=TRUE,
           ship=TRUE, dis="normal", plank=3, cline=TRUE, space=1.2,
           dot=TRUE, binz=c(11,23),
           icon=list(man%*%diag(c(5,1)), woman))

battleship(y=y, x=x, dtr=FALSE, fill=TRUE, xprop=FALSE,
           ship=TRUE, dis="normal", plank=4, cline=TRUE, space=1.2,
           dot=FALSE)

x <- rep(c(1:3),c(50,50,50)*3);y <- rep((rnorm(150)),3)
battleship(y=y,cens=0,x=x,binz=30,dtr=c(F,F,F),fill=T,xprop=F,
           #fillcol="lightblue",elicol="blue",
           space=3.3,dis="normal",plank=0.5,
           cline=c(T,F,F),clc="white",
           box=c(T,F,F),
           boxcol="black",
           dot=c(T,T,F),
           err=c(F,F,T),loc="mean",prec="2se",
           errcol=c("black","red","brown"),
           his=c(T,F,F),hiscol="darkgreen",
           vio=c(F,T,F),#viocol="green",
           ship=c(F,F,T))

# censored
x <- rep(c(1),c(80)*1);y <- rep((rnorm(80)),1)
cens <- rbinom(80,1,0.05)+(y>quantile(y,0.7))
battleship(y=y,cens=cens,x=x,dot=TRUE,dtr=FALSE,space=2.25,
           dis="normal",plank=1)

# Confluence
x <- rep(c(1,2,3),c(20,20,20)*1);y <- rep((rpois(20,5)),3)
battleship(y=y,x=x,dot=TRUE,dtr=FALSE,space=1.25,
           dis="poisson",confluence=c("Tufte","Tukey","Duerr"))

# Graphem = violin plot or density trace residual
x <- rep(c(1:2),c(50,50)*3);y <- rep((rnorm(150)),2)
battleship(y=y,x=x,space=2,dis="normal",dot=F,quant=NA,
 ship=T,vio=c(T,F),dtr=c(F,T))

# Graphem = error bar
y1 <- exp(rnorm(200,1,0.4));x1 <- rep(1,200)
battleship(y=y1,x=x1,space=2,dis="lognormal",dot=F,
 quant=NA,fill=T,ship=T,vio=T,dtr=T)

# Graphem = discret probability function bar plot
y2 <- rpois(30,5);x2 <- rep(2,30)
battleship(y=y2,x=x2,space=2,dis="poisson",dots=T,
 elicol="gray",fill=T,ship=T,shipcol="blue")

# Graphem = connecting line
x <- rep(c(1:5),10)
y <- rbinom(50,size=20,prob=c(0.05,0.2,0.5,0.8,0.95))
battleship(y=y,x=x,space=0.5,binz=30,dis="gamma",dot=T,
 elicol="gray",fill=T,ship=F,err=T,loc="mean",prec="2se",
 errcol="orange",connect=matrix(1:5,nrow=1),concol="black")
battleship(y=y,x=x,dis="binomial",trials=rep(20,5),dot=F,ship=F,
 err=F,loc="mean",prec="2se",errcol="orange",
 connect=matrix(1:5,nrow=1),concol="black")
battleship(y=y,cens=0,x=x,binz=89,dtr=F,fill=T,xprop=T,space=1.8,dot=T,ship=F)

# Aestetic = distribution
x <- rep(c(1:2),c(50,50)*3);y <- rep((rgamma(150,3)),2)
battleship(y=y,x=x,space=1.5,binz=55,dis=c("normal","lognormal"),
  dot=T,fill=T,elicol=c("darkgreen","darkgreen"),fillcol=c("green","green"),
  quant=NA,ship=T,vio=c(F,F),dtr=T)
battleship(y=y,x=x,space=1.5,binz=55,dot=T,
  fill=T,elicol=c("gray","gray"),fillcol=c("lightgray","lightgray"),
  quant=NA,ship=F,vio=T,dtr=T,sdsk=c(.2,.5))

# Aesthetic = bin numbers
battleship(y=y[1:150],x=x[1:150],space=2,binz=55,his=T,dot=F,
  fill=T,elicol=c("darkgreen","darkgreen"),fillcol=c("green","green"),
  quant=NA,ship=F,vio=c(F,F),dtr=T)
battleship(y=y[1:150],x=x[1:150],space=2,binz=12,his=T,dot=F,
  fill=T,elicol=c("darkgreen","darkgreen"),fillcol=c("green","green"),
  quant=NA,ship=F,vio=c(F,F),dtr=T)

# Mix of three genotypes
# Proportions Mendel
maf <- 0.1
p <- maf^2
pq <- 2*maf*(1-maf)
q <- (1-maf)^2
n <- 3000*c(q,pq,p)
x <- rep((1:length(n)),n);y <- rnorm(sum(n),x)
battleship(y=y,cens=0,x=x,dtr=F,fill=T,xprop=T,dot=T,ship=T,space=0.6)
CasesControls <- rep(c(1,2),1500)
battleship(y=y,cens=0,x=CasesControls,dis="mixnorm",genmix=T,mix=3,
           dtr=F,fill=T,xprop=T,dot=T,ship=T,space=1.5)

## End(Not run)

vonthein/illustrator documentation built on Nov. 7, 2019, 4:32 p.m.