Dear all,

I am using Sushi in order to plot some of our HiC data. I am reading a matrix of interactions, but I am getting the following error when using plotHic() function. Any help would be very much appreciated. Thank you.

 > y<-read.table("matrix-forR",header=TRUE, row.names=1)

> y[1:3,1:3]
       X0 X200000 X400000
0       0       0       0
200000  0       0       0
400000  0       0       0

chrom = "chr1"
chromstart = 50000000
chromend = 55000000

plotHic(y,chrom,chromstart,chromend)
phic = plotHic(y,chrom,chromstart,chromend)

Error in seq.default(min(vec), max(vec), length.out = num) :
  'from' cannot be NA, NaN or infinite

Thank you to those that read my email. The problem is solved. However, regarding "sushi" if I may add a new question :

particularly, I would like to display 2 HiC triangle plots (flipped and unflipped i.e. setting up "flip=TRUE" ) in order to allow an easy comparison.

the R code I use is the following (below), however it does not fully work in order to allow a side by side comparison,

any suggestions would be very welcome. thank you,

-- bogdan

---------- the R code ---------------------

chrom            = "chr11"
chromstart       = 500000
chromend         = 5050000

phic1 = plotHic(Sushi_HiC.matrix, chrom,chromstart, chromend, max_y = 20, zrange=c(0,28), palette=SushiColors(7))

phic2 = plotHic(Sushi_HiC.matrix, chrom,chromstart,chromend,max_y = 20, zrange=c(0,28), flip=TRUE, palette=topo.colors)

Many thanks to Doug Phanstiel for the insight. For those that are interested, a possible solution  by using the par(mfrow) command. 

# allow for 2 plots

par(mfrow=c(2,1))

# set margins

par(mar=c(1,1,1,1))

# move the labels closer to the axes

par(mgp=c(3,.5,0))

# plot the first  Hi-C plot

phic1 = plotHic(Sushi_HiC.matrix, chrom,chromstart, chromend, max_y = 20, zrange=c(0,28), palette=SushiColors(7))

# label the genome

labelgenome(chrom,chromstart,chromend,side=1,n=4,scale="Mb")

# plot the sencond  Hi-C plot

phic2 = plotHic(Sushi_HiC.matrix,chrom,chromstart,chromend,max_y = 20, zrange=c(0,28), flip=TRUE, palette=topo.colors)