draw_hic_contact_map {idr2d} | R Documentation |
Creates Hi-C contact maps to visualize the results of
estimate_idr2d_hic
.
draw_hic_contact_map( df, idr_cutoff = NULL, chromosome = NULL, start_coordinate = NULL, end_coordinate = NULL, title = NULL, values_normalized = FALSE, log_values = TRUE )
df |
output of
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idr_cutoff |
numeric; only show blocks with IDR < | ||||||||||||||||||
chromosome |
character; chromsome name or list of chromosome names to
be analyzed, e.g., UCSC chromosome 1, | ||||||||||||||||||
start_coordinate |
integer; only show contact map window between
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end_coordinate |
integer; only show contact map window between
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title |
character; plot title | ||||||||||||||||||
values_normalized |
logical; are read counts in value column
raw or normalized? Defaults to | ||||||||||||||||||
log_values |
logical; log-transform value column? Defaults to
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ggplot2 object; Hi-C contact map
idr_results_df <- estimate_idr2d_hic(idr2d:::hic$rep1_df, idr2d:::hic$rep2_df) draw_hic_contact_map(idr_results_df, idr_cutoff = 0.05, chromosome = "chr1")