draw_hic_contact_map {idr2d} | R Documentation

## 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")

[Package idr2d version 1.2.2 Index]