Question: genoPlotR in R
1
gravatar for br-barayah
5.3 years ago by
br-barayah10
United States
br-barayah10 wrote:

I’m working on plotting gene orders of two organisms using genoPlotR in R. I have my data downloaded from Nucleotide NCBI database in gb format. My data plots perfectly, however, names of genes appear to be crammed up, and I did not really find a way to make space between them or expand size of segment. 

my code is the following:

data files:

twelve<-try(read_dna_seg_from_file("//Users/location/12.gb"))
thirteen<-try(read_dna_seg_from_file("//Users/location/13.gb"))

annotation files:

ann_twelve<-annotation(x1=middle(twelve), text=twelve$name, rot = 30)
ann_thirteen<-annotation(x1=middle(thirteen), text=thirteen$name, rot = 30)

comparison file:

out144<-try(read_comparison_from_blast("/Users/location/out144.out"))

 

plotting:

plot_gene_map(dna_segs=list(twelve,thirteen),comparisons= list(out144),annotations=list(ann_twelve, ann_thirteen), annotation_height=0.8, gene_type="side_blocks",dna_seg_scale=TRUE,scale=FALSE, dna_seg_labels=c("twelve","thirteen"))

 

I have been trying different ways to modify segment size on the plotting code, but was not successful.

Here is how my plotted data looks like: 

 

 

code genoplotr sequence R plotting • 3.1k views
ADD COMMENTlink modified 5.1 years ago by xianghe.yan0 • written 5.3 years ago by br-barayah10
1
gravatar for komal.rathi
5.3 years ago by
komal.rathi3.5k
Children's Hospital of Philadelphia, Philadelphia, PA
komal.rathi3.5k wrote:

Use the argument annotation_cex=0.5 (or less) in plot_gene_map function.

ADD COMMENTlink modified 5.3 years ago • written 5.3 years ago by komal.rathi3.5k

I appreciate your reply. The font got smaller and gene names are separated now. I was able to view genes clearly when I downloaded the plot as PDF.

Thanks again!

ADD REPLYlink written 5.3 years ago by br-barayah10
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