Question: an error in ggbio: "Breaks and labels are different lengths"
0
gravatar for Bogdan
2.6 years ago by
Bogdan580
Palo Alto, CA, USA
Bogdan580 wrote:

Dear all, I am using ggbio in order to display the arcs (interactions) between genes; however, at some point in the code, i am getting the error : "Error in f(..., self = self) : Breaks and labels are different lengths".

Any suggestions please on how to fix it ? A piece of R code (running on R3.3.3 is below) :


i <- read.delim("file1",header=TRUE) 
interactions_granges <-GRanges (seqnames=i$chr, IRanges(i$start,i$end), strand="*", intensity=i$intensity, experiment=i$experiment)

er <-  rtracklayer::import("er", format = "bed")
enh <- rtracklayer::import("enhancers", format = "bed")

g <- read.delim("regions",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))  
   
   
gene_region <- autoplot(Homo.sapiens, which = region, color = "blue", fill = "blue",                             names.expr="SYMBOL") 

interactions_chr <- keepSeqlevels(interactions_granges,chr) ## 


hits <- findOverlaps(interactions_chr, region, type = 'within')
 
interactions_chr <- interactions_chr[queryHits(hits)] 

interactions_region <- autoplot(interactions_chr,geom="arch", aes(col=experiment, height=intensity, alpha = abs(intensity))) + xlim(region)

er_chr <- keepSeqlevels(er,chr) 
er_chr_plots <- autoplot(er_chr, geom="rect", fill ="red", col = "red" ) + scale_x_sequnit() + theme(axis.text.x = element_text(angle = 90, hjust = 1)) + xlim(region)

enh_chr <- keepSeqlevels(enh,chr)
enh_chr_plots <- autoplot(enh_chr, geom="rect", fill = "purple", color="purple") + scale_x_sequnit() + theme(axis.text.x = element_text(angle = 90, hjust = 1)) + xlim(region)

   

itracks <- tracks( "interactions" = interactions_region, "ER" = er_chr_plots, "ENH" = enh_chr_plots,

                            "genes" = gene_region, heights=c(4, 0.2, 0.2,  1) + 

                             xlim(region)  + theme(panel.background = element_rect(fill='transparent'))


   png(paste0("gene_", gene, "-" , chr, "-", start, "-", end, ".png" ), width=2000, height=1200)
   print(itracks) 
   dev.off()

 }

 

ggbio ggplot2 • 1.7k views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Bogdan580

Ayyy, nevermind, I think it was a mistake in my R script regarding the calculation of distances ;)

ADD REPLYlink written 2.6 years ago by Bogdan580
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