Question: How to remove the squished track in Give AlignmentTrack()
0
gravatar for gundalav
2.2 years ago by
gundalav300
La La Land
gundalav300 wrote:

I have the following code:

library(Gviz)
library(Mus.musculus)
library(data.table)
library(OrganismDbi)
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene


# Define bam file -----

adipose_bam <- "myfile.bam"

# Define region -----------------------------------------------------------
thechr <- "chr3"
st <- 116.108e6L
en <- 116.1317e6L 



# Define track ------------------------------------------------------------

itrack <- IdeogramTrack(
  genome = "mm10", chromosome = thechr
)

grtrack <- GeneRegionTrack(
  txdb,
  chromosome = thechr, start = st, end = en,
  showId = TRUE,
  name = "Gene Annotation"
)



gtrack <- GenomeAxisTrack(cex = 1) # set the font size larger

adipose_altrack <- AlignmentsTrack(
  adipose_bam,
  isPaired = TRUE, col.mates = "deeppink",
  name = "Adipose", fill = "blue", col = "blue"
)


plotTracks(
  list(itrack, gtrack, adipose_altrack, grtrack),
  from = st, to = en
)

It produces this plot:enter image description here

As define in the image how can I remove the squished track?

rna-seq • 462 views
ADD COMMENTlink modified 15 months ago by kathka0 • written 2.2 years ago by gundalav300
0
gravatar for kathka
15 months ago by
kathka0
kathka0 wrote:

This is probably way to late, but this post put me on the right track with my own work, so will provide this answer for others in the future..

Instead of using the AlignmentTracks class, use the DataTrack class to make a histogram coverage plot

adipose_covtrack <- DataTrack(test.bam,
                   genome = "mm10",
                   type = "h",  ## For histograms
                   name = "Adipose")

I haven't played around with the aesthetics, but the default setting provides blue fill.

ADD COMMENTlink modified 15 months ago • written 15 months ago by kathka0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1297 users visited in the last hour