Miscellaneous plots in R

install.packages("corrplot")

library(corrplot)

set.seed(12345)

A <- matrix(runif(100,1,100),nrow=10,ncol=10,byrow=T)

correlation_matrix <- cor(t(A), method="spearman")

corrplot(correlation_matrix)

col <- colorRampPalette(c("#BB4444", "#EE9988", "#FFFFFF", "#77AADD", "#4477AA"))
corrplot(correlation_matrix,
         method="shade", # visualisation method
         shade.col=NA, # colour of shade line
         tl.col="black", # colour of text label
         tl.srt=45, # text label rotation
         col=col(200), # colour of glyphs
         addCoef.col="black", # colour of coefficients
         order="AOE" # ordering method
         )

set.seed(31)
y <- matrix(rnorm(50),
            10,
            5,
            dimnames=list(paste("g", 1:10, sep=""),
                          paste("t", 1:5, sep=""))
            )
 
# data needs to be in long format
# install reshape if necessary
#install.packages("reshape")
library(reshape)
yy <- melt(y)
 
ggplot(yy, aes(x=X1, y=X2, fill=value)) +
  geom_raster() +
  scale_fill_gradient2(midpoint=0, mid="grey70", limits=c(-2,2))

> sim.I <- function(x)  {  # this is a closure
+   function(u) exp(-(x*u)^2/2) * x
+ }
> 
> g <- sim.I(10) # function used to simulate I_10
> U <- runif(1e5)
> Ts <- g(U)
> mean(Ts)
[1] 1.245262
> 0.5 * sqrt(2*pi)
[1] 1.253314
> 

ctc

ctc

heatmap(...) function can draw a heatmap, it's usage is:

heatmap(x, Rowv=NULL, Colv=if(symm)"Rowv" else NULL,
        distfun = dist, hclustfun = hclust,
        reorderfun = function(d,w) reorder(d,w),
        add.expr, symm = FALSE, revC = identical(Colv, "Rowv"),
        scale=c("row", "column", "none"), na.rm = TRUE,
        margins = c(5, 5), ColSideColors, RowSideColors,
        cexRow = 0.2 + 1/log10(nr), cexCol = 0.2 + 1/log10(nc),
        labRow = NULL, labCol = NULL, main = NULL,
        xlab = NULL, ylab = NULL,
        keep.dendro = FALSE, verbose = getOption("verbose"), ...)


x: Numeric matrix
Rowv: Row dendrogram
Colv: Column dendrogram

curve(expr, from = NULL, to = NULL, n = 101, add = FALSE,
      type = "l", xname = "x", xlab = xname, ylab = NULL,
      log = NULL, xlim = NULL, ...)

expr

from_to

add

demo(plotmath)
par(mar = c(4, 4, 2, 0.1))
plot(rnorm(100), rnorm(100),
  xlab = expression(hat(mu)[0]), ylab = expression(alpha^beta),
  main = expression(paste("Plot of ", alpha^beta, " versus ", hat(mu)[0])))

par(mar = c(4, 4, 2, 0.1))
x_mean <- 1.5
x_sd <- 1.2
hist(rnorm(100, x_mean, x_sd),
  main = substitute(
    paste(X[i], " ~ N(", mu, "=", m, ", ", sigma^2, "=", s2, ")"),
    list(m = x_mean, s2 = x_sd^2)
  )
)