chicane (version 0.1.8)

create.locus.plot: create.locus.plot

Description

Create a file compatible with WashU Epigenome Browser from CHiCANE interaction calls.

Usage

create.locus.plot(
  genome = "hg38",
  chr = NULL,
  start = NULL,
  end = NULL,
  gene.data = NULL,
  genomic.features = NULL,
  feature.name = NULL,
  fdr.filter = 0.05,
  interaction.data = NULL,
  file.name = NULL,
  height = 5.5,
  width = 8.5,
  track.heights = c(0.2, 0.5, 0.8, 0.5, 1.5, 2),
  ...
)

Arguments

genome

Name of genome build (e.g. 'hg38' or 'hg37')

chr

Chromosome number for desired locus including 'chr' (e.g. 'chr1')

start

Start coordinate of desired locus

end

End coordinate of desired locus

gene.data

Path to chosen genome annotation file in .gtf format

genomic.features

Path to BED file with coordinates of desired feature track

feature.name

Title to appear above genomic features

fdr.filter

Q-value filter threshold for interaction calls to be included

interaction.data

Path to unfiltered CHiCANE calls output

file.name

Path to output file

height

Height in inches for desired plot

width

Width in inches of desired plot

track.heights

Vector of length 6 indicating desired height of individual tracks

…

Any additional parameters to Gviz::plotTracks

Value

TRUE if plot was successfully created

Examples

# NOT RUN {
# In order to conserve memory only significant interactions are included in example 
# interaction.data file. However, in order to show raw counts, unfiltered calls should be 
# included and only significant interactions (as set by fdr.filter) wil be displayed

gene.data <- system.file('extdata', 'gencode_2q35.gtf', package = 'chicane');
genomic.features <- system.file('extdata', '2q35.bed', package = 'chicane');
interaction.data <- system.file(
  'extdata', 'T47D_2q35_filtered_chicane_calls.txt', 
  package = 'chicane'
  );
file.name <- file.path(tempdir(), "chr2_interactions.pdf");

# }
# NOT RUN {
create.locus.plot(
   genome = 'hg38', 
   chr = 'chr2', 
   start = 216600000,
   end = 217200000,
   gene.data = gene.data,
   genomic.features = genomic.features,
   feature.name = 'baits',
   interaction.data = interaction.data,
   file.name = file.name,
   collapseTranscripts = TRUE,
   shape = "arrow"
   );
 
# }
# NOT RUN {
# }