converts to factor and then numeric

Description

Converts a vector of characters into factors and then converts these into numeric.

Usage

as.fumeric(x, levels = unique(x))

Arguments

Author(s)

Rafael A. Irizarry

Examples

group = c("a","a","b","b")
plot(seq_along(group),col=as.fumeric(group))

bartab

Description

Plot the overlap of three groups with a barplot

Usage

bartab(x, y, z, names, skipNone = FALSE, ...)

Arguments

Author(s)

Michael I. Love

Examples

set.seed(1)
x <- sample(c(FALSE,TRUE), 10, replace=TRUE)
y <- sample(c(FALSE,TRUE), 10, replace=TRUE)
z <- sample(c(FALSE,TRUE), 10, replace=TRUE)
bartab(x,y,z,c("X","Y","Z"))

image of a matrix

Description

Produces an image of a matrix which matches the natural orientation.

Usage

imagemat(
  x,
  col = colorRampPalette(c("white", "grey50"))(9),
  las = 1,
  xlab = "",
  ylab = "",
  ...
)

Arguments

Author(s)

Michael I. Love

Examples

x <- matrix(c(1,0,0,0,1,
              1,1,0,1,1,
              1,0,1,0,1,
              1,0,0,0,1,
              1,0,0,0,1),
ncol=5,byrow=TRUE)

imagemat(x)

image with sorted rows

Description

the rows are sorted such that the first column has 2 blocks, the second column has 4 blocks, etc. see example("imagesort")

Usage

imagesort(x, col = c("white", "black"), ...)

Arguments

Author(s)

Michael I. Love

Examples

x <- replicate(4,sample(0:1,40,TRUE))
imagesort(x)

Install or update Bioconductor and CRAN packages

Description

This function is simply a wrapper for link[BiocManager]{install}. If BiocManager is not installed it it automatically installed.

Usage

install_bioc(...)

Arguments

Details

If BiocManager is installed you can simply call BiocManager::install instead.

Author(s)

Rafael A. Irizarry

Examples

  install_bioc("affy")

What are the largest objects in memory?

Description

This function lists all the objects in the global environmnet and lists the n largest.

Usage

largeobj(n = 5, units = "Mb")

Arguments

Value

a named character string of the size of the 'n' largest objects

Author(s)

Michael I. Love

Examples

x<-rnorm(10^5)
y<-rnorm(10^6)
z<-rnorm(2*10^6)
w<-rnorm(3*10^6)
largeobj(n=3)

Bland Altman plot aka MA plot

Description

Takes two vectors x and y and plots M=y-x versus A=(x+y)/2. If the vectors a more longer than length n the data is sampled to size n. A smooth curve is added to show trends.

Usage

maplot(
  x,
  y,
  n = 10000,
  subset = NULL,
  xlab = NULL,
  ylab = NULL,
  curve.add = TRUE,
  curve.col = 2,
  curve.span = 1/2,
  curve.lwd = 2,
  curve.n = 2000,
  ...
)

Arguments

Author(s)

Rafael A. Irizarry

Examples

n <- 10000
signal <- runif(n,4,15)
bias <- (signal/5 - 2)^2 
x <- signal + rnorm(n)
y <- signal + bias + rnorm(n)  
maplot(x,y)

mypar

Description

Called without arguments, this function optimizes graphical parameters for the RStudio plot window. bigpar uses big fonts which are good for presentations.

Usage

mypar(
  a = 1,
  b = 1,
  brewer.n = 8,
  brewer.name = "Dark2",
  cex.lab = 1,
  cex.main = 1.2,
  cex.axis = 1,
  mar = c(2.5, 2.5, 1.6, 1.1),
  mgp = c(1.5, 0.5, 0),
  ...
)

Arguments

Author(s)

Rafael A. Irizarry

Examples

mypar()
plot(cars)
bigpar()
plot(cars)

plclust in colour

Description

Modifiction of plclust for plotting hclust objects in *in colour*!

Usage

myplclust(
  hclust,
  labels = hclust$labels,
  lab.col = rep(1, length(hclust$labels)),
  hang = 0.1,
  xlab = "",
  sub = "",
  ...
)

Arguments

Author(s)

Eva KF Chan

Examples

data(iris)
hc <- hclust( dist(iris[,1:4]) )
myplclust(hc, labels=iris$Species,lab.col=as.numeric(iris$Species))

nullplot

Description

Make an plot with nothing in it

Usage

nullplot(x1 = 0, x2 = 1, y1 = 0, y2 = 1, xlab = "", ylab = "", ...)

Arguments

Examples

nullplot()

peek at the top of a text file

Description

this returns a character vector which shows the top n lines of a file. Note: I realized after the fact that this is essentially a duplicate of the base R function readLines.

Usage

peek(x, n = 2)

Arguments

Author(s)

Michael I. Love

Examples

filename <- tempfile()
x<-matrix(round(rnorm(10^4),2),1000,10)
colnames(x)=letters[1:10]
write.csv(x,file=filename,row.names=FALSE)
peek(filename)

population standard deviation

Description

Returns the population standard deviation. Note that sd returns the unbiased sample estimate of the population standard deviation. It simply multiplies the result of var by (n-1) / n with n the population size and takes the square root.

Usage

popsd(x, na.rm = FALSE)

Arguments

population variance

Description

Returns the population variance. Note that var returns the unbiased sample estimate of the population variance. It simply multiplies the result of var by (n-1) / n with n the population size.

Usage

popvar(x, ...)

Arguments

Examples

x <- c(0,1) ##variance should be 0.5^2=0.25
var(x) 
popvar(x)

smart boxplot

Description

draws points or boxes depending on sample size

Usage

sboxplot(x, ...)

Arguments

Examples

sboxplot(list(a=rnorm(15),b=rnorm(75),c=rnorm(10000)))

smooth histogram

Description

a smooth histogram with unit indicator (we're simply scaling the kernel density estimate). The advantage of this plot is its interpretability since the height of the curve represents the frequency of a interval of size unit around the point in question. Another advantage is that if z is a matrix, curves are plotted together.

Usage

shist(
  z,
  unit,
  bw = "nrd0",
  n,
  from,
  to,
  plotHist = FALSE,
  add = FALSE,
  xlab,
  ylab = "Frequency",
  xlim,
  ylim,
  main,
  ...
)

Arguments

Examples

set.seed(1)
x = rnorm(50)
par(mfrow=c(2,1))
hist(x, breaks=-5:5)
shist(x, unit=1, xlim=c(-5,5))

split it

Description

Creates an list of indexes for each unique entry of x

Usage

splitit(x)

Arguments

Examples

x <- c("a","a","b","a","b","c","b","b")
splitit(x)

smart plot

Description

if n > 10,000, make a random subset of 10,000 and plot. You can also specify a specific subset to plot. If length of subset is larger than n, a random sample is still used to reduce data size.

Usage

splot(x, y, n = 10000, subset = NULL, xlab = NULL, ylab = NULL, ...)

Arguments

Examples

x <- rnorm(1e5)
y <- rnorm(1e5)
splot(x,y,pch=16,col=rgb(0,0,0,.25))

Better defaults for stripchart

Description

This simply calls stripchart but specifies a vertical plot with jitter and using pch=1.

Usage

stripplot(...)

Arguments

Value

a plot