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)

}

-----------------------------------------------

## Friday, February 29, 2008

## Wednesday, February 27, 2008

### 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

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

## Monday, February 25, 2008

### 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

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

## Saturday, February 9, 2008

### 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))

[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))

## Monday, February 4, 2008

### R points

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