I see!: R

mm - milimeter from where sample was put into gele
bp - base pair

You need:

Text file with marker sizes and distances (marker.csv)
Text file with distance of your sample (sample.csv)

# R Script file get_bp_from_mm.R:

getbpfrommm <- function(marker, unknown, unknown.filename){
# log bp of marker
markerlog <- marker
markerlog$bp <- log(markerlog$bp)

# make linear model
marker.lm <- lm(markerlog$bp ~ markerlog$mm)

b=coef(marker.lm)[1]
m=coef(marker.lm)[2]

unknown.bp <- c()

for(unknown.mm.i in unknown){
    unknown.bp.i = round(exp(m*unknown.mm.i+b))
    unknown.bp <- c(unknown.bp, unknown.bp.i)}

unknown.bp.mm <- cbind(unknown, unknown.bp)
colnames(unknown.bp.mm) <- c("mm", "bp")

print(unknown.bp.mm)

write.table(unknown.bp.mm, file=paste(unknown.filename, "with_bp.csv", sep="_"), quote=FALSE, sep="\t", row.names=FALSE, col.names=TRUE)
}

#read command line arguments
args <- commandArgs(trailingOnly = TRUE)
marker <- read.delim(args[1])
unknown <- read.delim(args[2])

getbpfrommm(marker, unknown, args[2])

# Invoke from command line
$ cat marker.csv
mm    bp
132.60    75
116.80    200
106.20    300
95.60    400
89.20    500
72.20    700
62.80    1000
48.30    1500
38.40    2000
19.1    5000

$ cat sample.csv
mm
103.4
98.8

$ Rscript get_bp_from_mm.R marker.csv sample.csv
     mm bp
1 103.4 272
2 98.8 317

$ cat sample.csv_with_bp.csv
mm    bp
103.4    272
98.8    317

Wikipedia has a very nice Venn diagram for five sets. I use this svg file to automatically create a Venn diagram displaying the number of intersecting elements of five sets.

Number of intersecting elements

For this we need the number of intersecting elements for all possible set combinations, in my example it looks like this:

numbers.txt

A 13644

B 14729

C 14690

D 13725

E 13742

AB 3689

AC 3616

AD 3523

AE 3496

BC 14281

BD 12852

BE 12694

CD 13215

CE 13060

DE 13563

ABC 3609

ABD 3507

ABE 3480

ACD 3513

ACE 3487

ADE 3496

BCD 12849

BCE 12694

BDE 12694

CDE 13056

ABCD 3506

ABCE 3480

ABDE 3480

ACDE 3487

BCDE 12694

ABCDE 3480

To get these numbers I used a small R script and formatted the output with a little bit of TextWrangler and grep to look like in the file numbers.txt

Here is the short R script:

A <- read.delim('Info1.csv')$name

B <- read.delim('Info2.csv')$name

C <- read.delim('Info3.csv')$name

D <- read.delim('Info4.csv')$name

E <- read.delim('Info5.csv')$name

# all sets

print(paste("A",length(A)))

print(paste("B",length(B)))

print(paste("C",length(C)))

print(paste("D",length(D)))

print(paste("E",length(E)))

# all combinations of two sets

print(paste("A, B", length(intersect(A, B))))

print(paste("A, C", length(intersect(A, C))))

print(paste("A, D", length(intersect(A, D))))

print(paste("A, E", length(intersect(A, E))))

print(paste("B, C", length(intersect(B, C))))

print(paste("B, D", length(intersect(B, D))))

print(paste("B, E", length(intersect(B, E))))

print(paste("C, D", length(intersect(C, D))))

print(paste("C, E", length(intersect(C, E))))

print(paste("D, E", length(intersect(D, E))))

# all combinations of three sets

print(paste("A, B, C", length(intersect(A, intersect(B, C)))))

print(paste("A, B, D", length(intersect(A, intersect(B, D)))))

print(paste("A, B, E", length(intersect(A, intersect(B, E)))))

print(paste("A, C, D", length(intersect(A, intersect(C, D)))))

print(paste("A, C, E", length(intersect(A, intersect(C, E)))))

print(paste("A, D, E", length(intersect(A, intersect(D, E)))))

print(paste("B, C, D", length(intersect(B, intersect(C, D)))))

print(paste("B, C, E", length(intersect(B, intersect(C, E)))))

print(paste("B, D, E", length(intersect(B, intersect(D, E)))))

print(paste("C, D, E", length(intersect(C, intersect(D, E)))))

# all combinations of four sets

print(paste("A, B, C, D", length(intersect(A, intersect(B, intersect(C, D))))))

print(paste("A, B, C, E", length(intersect(A, intersect(B, intersect(C, E))))))

print(paste("A, B, D, E", length(intersect(A, intersect(B, intersect(D, E))))))

print(paste("A, C, D, E", length(intersect(A, intersect(C, intersect(D, E))))))

print(paste("B, C, D, E", length(intersect(B, intersect(C, intersect(D, E))))))

# combination of five sets

print(paste("ABCDE", length(intersect(A, intersect(B, intersect(C, intersect(D, E)))))))

Getting these numbers into the diagram

Since the svg file only consists of 51 lines, I display it here:

<?xml version="1.0" encoding="UTF-8"?>

<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">

<title>Radially-symmetrical Five-set Venn Diagram</title>

<desc>Devised by Branko Gruenbaum and rendered by CMG Lee.</desc>

<defs>

</g>

</defs>

<text x="0" y="0" dy="0.7ex">ABCDE</text>

</g>

</svg>

You can see, that the names of the different overlapping fields are annotated as "A", "B", "AB", and so forth. Hence, I can just replace them with sed, to display my own data!

This I do with the following bash/sed command:

while read LINE

NAME=$( echo $LINE | awk '{print $1 }')

NUMB=$( echo $LINE | awk '{print $2 }')

echo $NAME $NUMB

sed -i tmp "s/\>${NAME}\</\>${NUMB}\</g" venn.svg

echo "sed -i tmp "s/\>\${NAME}\</\>\${NUMB}\</g" venn.svg"

done < 'numbers.txt'

The altered Venn diagram

The output is indeed exactly what I wanted:

Of course, I still need to adapt the font size, but thanks to sed, this won't be a big issue.

I see!

2014-04-06

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2013-07-19

How to automatically create Venn diagram for five sets

Number of intersecting elements

Getting these numbers into the diagram

The altered Venn diagram

2012-11-13

How to split a string in R using strsplit

2012-10-31

R: Function to perform t-test on all possible combinations of columns in a dataframe

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