draw_hic_contact_map: Create Hi-C contact map

In kkrismer/idr2d: Irreproducible Discovery Rate for Genomic Interactions Data

Create Hi-C contact map

Description

Creates Hi-C contact maps to visualize the results of estimate_idr2d_hic.

Usage

draw_hic_contact_map(
  df,
  idr_cutoff = NULL,
  chromosome = NULL,
  start_coordinate = NULL,
  end_coordinate = NULL,
  title = NULL,
  values_normalized = FALSE,
  log_values = TRUE
)

Arguments

df	output of estimate_idr2d_hic, a data frame with the following columns: column 1: interaction character; genomic location of interaction block (e.g., "chr1:204940000-204940000") column 2: value numeric; p-value, FDR, or heuristic used to rank the interactions column 3: "rep_value" numeric; value of corresponding replicate interaction column 4: "rank" integer; rank of the interaction, established by value column, ascending order column 5: "rep_rank" integer; rank of corresponding replicate interaction column 6: "idr" integer; IDR of the block and the corresponding block in the other replicate
idr_cutoff	numeric; only show blocks with IDR < idr_cutoff, shows all blocks by default
chromosome	character; chromsome name or list of chromosome names to be analyzed, e.g., UCSC chromosome 1, "chr1", defaults to all chromosomes (chromosome = NULL)
start_coordinate	integer; only show contact map window between "start_coordinate" and "end_coordinate", by default shows entire chromosome
end_coordinate	integer; only show contact map window between "start_coordinate" and "end_coordinate", by default shows entire chromosome
title	character; plot title
values_normalized	logical; are read counts in value column raw or normalized? Defaults to FALSE
log_values	logical; log-transform value column? Defaults to TRUE

Value

ggplot2 object; Hi-C contact map

Examples

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")

kkrismer/idr2d documentation built on Feb. 7, 2024, 2:23 p.m.