charting maps

[rtadmorl]

Hello,
Does anyone have a reccomendation of a software that will visualize the map created by LEPMAP2?
My map files are ready and I would like to chart my LGs.
Many thanks!
Roni Tadmor-Levi
Hebrew University

[Federico Calboli]

Hi, I just wrote the code in R especially. If you email me at

federico DOT calboli AT helsinki DOT fi

I can send you the code. Please note it works 'for my pipeline', so you might need to adapt it, possibly quite a bit.

[Pasi Rastas]

Dear Roni Tadmor-Levi,

Thank you for your question.

Sorry I cannot help as I have not ever charted my maps it that way. Maybe you or I could ask Federico as he did the charting in the Lep-MAP2 paper.

Cheers,
Pasi

[rtadmorl]

Many thanks to you both, I will e-mail Federico.

[Federico Calboli]

Here is the code I used, for reference.

PART 1: turn LM2 output in csv files

run this part in a bash shell (you need to be in the directory the files have been stored in).

sed -i '' $'s/\t/,/g' .txt
sed -i '' 's/)/,/g' .txt
sed -i '' 's/(//g' *.txt

for file in *.txt; do
mv "$file" "basename $file .txt.csv"
done

for file in *csv; do
sed -i '' '1,2d' $file
done

for file in *csv; do
sed -i '' '$d' $file
done

sed -i '' 's/#//' *csv

PART 2: actually plot the chromosomes:

run the following in R NOTE I HAVE 21 chromosomes, change the instances of 21 to your number of chromosomes

mf = vector(length = 21, mode = 'list')
sa = vector(length = 21, mode = 'list')

for (i in 1:21){
mf[[i]] = read.csv(paste('chr', i, '.MF.csv', sep = ''), na.strings = '', col.names = c('marker', 'm_map', 'f_map','error', 'duplicate','phase'))
sa[[i]] = read.csv(paste('chr', i, '.SA.csv', sep = ''), na.strings = '', col.names = c('marker', 'map', 'map','error', 'duplicate', 'phase'))
}

mfx= lapply(mf, function(x){x[!is.na(x$duplicate),1]})
sax = lapply(sa, function(x){x[!is.na(x$duplicate),1]})
xx = unique(c(unlist(mfx), unlist(sax)))

mf = lapply(mf, function(x){x[!is.element(x[,1], xx), ]})
sa = lapply(sa, function(x){x[!is.element(x[,1], xx), ]})

this should print out TRUE in all instances

for(i in 1:21){
print(c(as.character(i), identical(mf[[i]][,1], sa[[i]][,1])))
}

for(i in 1:21){
mf[[i]]$LG = i
}

for(k in 1:21){
mf[[k]] = data.frame(LG = mf[[k]]$LG, marker = mf[[k]][,1], m_map = mf[[k]][,2], f_map = mf[[k]][,3], map = sa[[k]][,2], duplicate = mf[[k]][,5], error = mf[[k]][,4], phase = mf[[k]][,6])
}

wholemap = NULL
for(i in 1:21){
wholemap = rbind(wholemap, mf[[i]])
}

wholemapm.maps = tapply(wholemap$m_map, wholemap$LG, unique)
wholemapf.maps = tapply(wholemap$f_map, wholemap$LG, unique)
wholemap.maps = tapply(wholemap$map, wholemap$LG, unique)

plot.maps = function(chroms, main = 'Cromosome Plot', xlim = NULL, ylab = 'Linkage Group'){
upper.l = max(unlist(chroms))
lower.l = 0
lower.l2 = lower.l - upper.l0.025
upper.l2 = upper.l1.025
if(length(xlim) == 2)
nexlim = xlim
else
nexlim = c(lower.l2, upper.l2)
plot(chroms[[1]], rep(1, length(chroms[[1]])), pch = '|', xlim = nexlim, ylim = c(0,22), xlab = 'cM', ylab = ylab, main = main, type = 'n', yaxt = 'n')
axis(side = 2, at = 1:21, labels = 1:21, las= 1)

##### axis(side = 1, at = (seq(lower.l, upper.l, by = 25)))

for(i in 1:21){
maxy = max(chroms[[i]])
segments(0.75, i, maxy-0.75, i, col = 'lightgrey', lwd = 7)
points(chroms[[i]], rep(i, length(chroms[[i]])), pch = '|')
}
}

par(mfrow = c(1,3))

you might have to adjust the xlims

plot.maps(wholemapm.maps, main = 'Male', xlim = c(0,420))
plot.maps(wholemapf.maps, main = 'Female', xlim = c(0,420))
plot.maps(wholemap.maps, main = 'Sex Averaged', xlim = c(0,420))

[Stephen Trevoy]

Hi there,

Some questions for formatting the .csv files so the R script runs properly:

1) Do chromosomes need to be separated into their own .csv files?
2) Do families need to be separated into their own .csv files?