Dear all,

I would appreciate a help with writing for a "for loop" with "autoplot" function :

I read a list of genes (chr, start, end) from a file, and would like to use the AUTOPLOT function to display each of these genes (in ggbio package) : but I am not obtaining any result  . Any insights ? thank you,

-- bogdan

the R script is the following :

g <- read.delim("list_GENES",header=TRUE, stringsAsFactors=FALSE)

for (j in 1:nrow(g))
{
   chr <- g[j,]$chr ;
   start <- g[j,]$start ;
   end <- g[j,]$end ;
   gene <- g[j,]$gene ;

   region <- GRanges(chr, IRanges(start,end)) ;

    png("gene.png")

autoplot(Homo.sapiens, which = region, stat = "reduce", color = "blue", fill = "blue", names.expr="SYMBOL")
    dev.off()
 
}

where the file "list_GENES" is in the format :

chr    start    end    gene
chr16    8663964    8855703    ABAT
chr11    77484160    77741533    ALG8
chr11    69024132    69186057    CCND1
chr1    109424543    109642035    CELSR2
chr15    99517335    99748326    CHSY1
chr6    151733634    152220321    ESR1

You need to wrap your call to autoplot() with a call to print(), and you need to have different file names for each png:

png(paste0(gene, ".png"))

print(autoplot(Homo.sapiens, which = region, stat = "reduce", color = "blue", fill = "blue", names.expr="SYMBOL"))

dev.off()

Dear James,

thanks for the prompt help. It works nicely ;) happy weekend !

-- bogdan