plotStream: Stream plot

In marchtaylor/sinkr: Collection of functions with emphasis in multivariate data analysis

Stream plot

Description

plotStream makes a "stream plot" where each y series is plotted as stacked filled polygons on alternating sides of a baseline. A random wiggle is applied through the arguments frac.rand and spar such that each plot will be different unless preceeded by a random seed (e.g. set.seed(1)).

Usage

plotStream(
  x,
  y,
  order.method = "as.is",
  frac.rand = 0.1,
  spar = 0.2,
  center = TRUE,
  ylab = "",
  xlab = "",
  border = NULL,
  lwd = 1,
  col = rainbow(length(y[1, ])),
  ylim = NULL,
  ...
)

Arguments

x	A vector of values
y	A matrix of data series (columns) corresponding to x
order.method	Method of ordering y plotting order. One of the following: c("as.is", "max", "first"). "as.is" - plot in order of y column. "max" - plot in order of when each y series reaches maximum value. "first" - plot in order of when each y series first value > 0.
frac.rand	Fraction of the overall data "stream" range used to define the range of random wiggle (uniform distrubution) to be added to the baseline g0
spar	Setting for smooth.spline function to make a smoothed version of baseline "g0"
center	Logical. If TRUE, the stacked polygons will be centered so that the middle, i.e. baseline (g0), of the stream is approximately equal to zero. Centering is done before the addition of random wiggle to the baseline.
ylab	y-axis labels
xlab	x-axis labels
border	Border colors for polygons corresponding to y columns (will recycle) (see ?polygon for details)
lwd	Border line width for polygons corresponding to y columns (will recycle)
col	Fill colors for polygons corresponding to y columns (will recycle).
ylim	y-axis limits. If ylim=NULL, defaults to c(-0.7, 0.7)*max(apply(y,1,sum))
...	Other plot arguments

Value

A plot with stream visualization added

Examples

#Create data
set.seed(1)
m <- 500
n <- 30
x <- seq(m)
y <- matrix(0, nrow=m, ncol=n)
colnames(y) <- seq(n)
for(i in seq(ncol(y))){
 mu <- runif(1, min=0.25*m, max=0.75*m)
 SD <- runif(1, min=5, max=20)
 TMP <- rnorm(1000, mean=mu, sd=SD)
 HIST <- hist(TMP, breaks=c(0,x), plot=FALSE)
 fit <- smooth.spline(HIST$counts ~ HIST$mids)
 y[,i] <- fit$y
}
y <- replace(y, y<0.01, 0)

#Ex.1 : Color by max value)
pal <- colorRampPalette(c(rgb(0.85,0.85,1), rgb(0.2,0.2,0.7)))
BREAKS <- pretty(apply(y,2,max),8)
LEVS <- levels(cut(1, breaks=BREAKS))
COLS <- pal(length(BREAKS )-1)
z <- val2col(apply(y,2,max), col=COLS)

#Plot order = "as.is"
plotStream(x,y, xlim=c(100, 400), center=TRUE, spar=0.3, frac.rand=0.2, 
col=z, border="white", lwd=0.5)

#Plot order = "max"
plotStream(x,y, xlim=c(100, 400), center=TRUE, order.method="max", spar=0.3, 
frac.rand=0.2, col=z, border="white", lwd=0.5)

#Ex. 2 : Color by first value
ord <- order(apply(y, 2, function(r) min(which(r>0))))
y2 <- y[, ord]
pal <- colorRampPalette(c("blue", "cyan", "yellow", "red"))
z <- pal(ncol(y2))

#Plot order = "as.is"
plotStream(x,y2, xlim=c(100, 400), center=FALSE, spar=0.1, frac.rand=0.05, 
col=z, border=1, lwd=0.25)

#Plot order = "max"
plotStream(x,y2, xlim=c(100, 400), center=FALSE, order.method="max", spar=0.1, 
frac.rand=0.05, col=z, border=1, lwd=0.25)

#Extremely wiggly, no borders, no box, no axes, black background
op <- par(bg=1, mar=c(0,0,0,0))
plotStream(x,y2, xlim=c(100, 400), center=FALSE, spar=0.3, frac.rand=1, col=z, 
border=NA, axes=FALSE)
par(op)

marchtaylor/sinkr documentation built on July 4, 2022, 5:48 p.m.