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Question: about XLIM() in ggbi
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gravatar for Bogdan
3.9 years ago by
Bogdan520
Palo Alto, CA, USA
Bogdan520 wrote:

Dear all, and Tengfei,
 

I would like to plot some interactions as ARCHES within SPECIFIC GENE AREAS (eg NRIP1 :chr21: 15238712 - 15437750) from a file that contains interactions on ALL the chromosomes in the human genome :

please could you advise on how to use the XLIM() function, as all the chromosomes are displayed in the output figure, and not only the NRIP1 area I am interested in. thanks,

-- bogdan

ps: the code I am using is : 

library("ggplot2")
library("GenomicFeatures")
library("ggbio")
library("Gviz")
library("rtracklayer")

#-----uploading GENES------------------------
library(TxDb.Hsapiens.UCSC.

hg18.knownGene)
txdb<-TxDb.Hsapiens.UCSC.hg18.knownGene


# --- To add a region -- namely region X ----

chr <- "chr21"
start <- 15238712 
end <- 15437750

gene_name <- "NRIP1"

region <- GRanges(chr, IRanges(start,end))
gene <- autoplot(txdb, which = region,  color = "blue", fill = "blue", names.expr="tx_name:gene_id")

# ------------ reading the interactions -----------------------

r<-read.delim("FILE_with_ALL_INTERACTIONS",header=TRUE)

rr<-GRanges(seqnames=r$chr,IRanges(r$start,r$end),strand="*",intensity=r$intensity,experiment=r$experiment)
 
rrr <- autoplot(rr,geom="arch",aes(col=experiment,height=intensity,alpha = abs(intensity))) + xlim(region)


# ----------------- plotting these tracks ---------------------------------------------

tracks("genes" = gene, "interactions" = rrr, heights=c(1,6)) + xlim(region) + theme(panel.background = element_rect(fill='transparent'))

ADD COMMENTlink written 3.9 years ago by Bogdan520
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