R Create Venn diagram

Using the package limma to draw the venn diagram.

Code:
-----------------------------------------------
A1 <- c("A", "B");
A2 <- c("A", "B", "C");
A3 <- c("D", "B");

library(limma);
SET.list <- list(A1=A1, A2=A2, A3=A3);
len <- length(SET.list);
all.unique <- unique(unlist(SET.list));
tmp <- matrix(0, ncol=len, nrow=length(all.unique));
colnames(tmp) <- names(SET.list);
rownames(tmp) <- all.unique;
for(ith in 1:len){
tmp[SET.list[[ith]], ith] <- 1;
}
count.sum <- apply(tmp, 1, sum);
count.sum
if(len < 4){
windows();
vennDiagram(vennCounts(tmp), main = "gene.intersection", cex = 1)
}
-----------------------------------------------

R colors

R colors in a way that is intended to aid finding colors by name, or by index in the It contains 657 kinds of colors:
For example:
--------------------------------------------------------------------------
> colors()[c(552,254,26)]
[1] "red" "green" "blue"
> colors()[grep("red",colors())]
[1] "darkred" "indianred" "indianred1" "indianred2"
[5] "indianred3" "indianred4" "mediumvioletred" "orangered"
[9] "orangered1" "orangered2" "orangered3" "orangered4"
[13] "palevioletred" "palevioletred1" "palevioletred2" "palevioletred3"
[17] "palevioletred4" "red" "red1" "red2"
[21] "red3" "red4" "violetred" "violetred1"
[25] "violetred2" "violetred3" "violetred4"
> colors()[grep("sky",colors())]
[1] "deepskyblue" "deepskyblue1" "deepskyblue2" "deepskyblue3"
[5] "deepskyblue4" "lightskyblue" "lightskyblue1" "lightskyblue2"
[9] "lightskyblue3" "lightskyblue4" "skyblue" "skyblue1"
[13] "skyblue2" "skyblue3" "skyblue4"
> col2rgb("yellow")
[,1]
red 255
green 255
blue 0
--------------------------------------------------------------------
A full set of color image is here, download from the reference site.



The chart can be generate by the code:

setwd("C:/");
source("http://research.stowers-institute.org/efg/R/Color/Chart/ColorChart.R")

and check the pdf file under your your C: directory.


Reference:
http://research.stowers-institute.org/efg/R/Color/Chart/index.htm
http://www.stat.columbia.edu/~tzheng/files/Rcolor.pdf

Letter counter using R

We can use R to do something that they are not designed to do so, like the letter counting using R.

In R, the package "seqinr" is design to do the data analysis for DNA sequence and protein sequence.

For example, in a txt file "tmp.txt", we have a

R string manipulation

> x <- c("a", "b", "c"); > paste(x, 1:3, sep="..");
[1] "a..1" "b..2" "c..3"
> paste(x, collapse="..");
[1] "a..b..c"
> strsplit("a.b.c", ".", fixed = TRUE)
[[1]]
[1] "a" "b" "c"

> unlist(strsplit("a.b.c", ".", fixed = TRUE));
[1] "a" "b" "c"
> strtrim(c("abcdef", "abcdef", "abcdef"), c(1,5,10))
[1] "a" "abcde" "abcdef"
> substr("abcdef",2,4)
[1] "bcd"
> substring("abcdef",c(1, 3), c(2, 6))
[1] "ab" "cdef"
> strtrim(c("abcdef", "abcdef", "abcdef"), c(1,5,10))
[1] "a" "abcde" "abcdef"

#############################################
x <- c("a", "b", "c");
paste(x, 1:3, sep="..");
paste(x, collapse="..");
strsplit("a.b.c", ".", fixed = TRUE)
unlist(strsplit("a.b.c", ".", fixed = TRUE));
strtrim(c("abcdef", "abcdef", "abcdef"), c(1,5,10))
substr("abcdef",2,4)
substring("abcdef",c(1, 3), c(2, 6))
strtrim(c("abcdef", "abcdef", "abcdef"), c(1,5,10))

R points

R use pch to control the point symbol. This can either be a single character or an integer code for one of a set of graphics symbols. The full set of S symbols is available with pch=0:18.