Description Usage Arguments Value Author(s) Examples
View source: R/create.locus.plot.R
Create a file compatible with WashU Epigenome Browser from CHiCANE interaction calls.
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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 |
TRUE if plot was successfully created
Andrea Gillespie, Syed Haider
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | # 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");
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"
);
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