DiffPlot {TADCompare} | R Documentation

## Visualization of differential TAD boundaries

### Description

Visualization of differential TAD boundaries

### Usage

    DiffPlot(
      tad_diff,
      cont_mat1,
      cont_mat2,
      resolution,
      start_coord,
      end_coord,
      pre_tad = NULL,
      show_types = TRUE,
      point_size = 3,
      max_height = 25,
      rel_heights = c(2, 1),
      palette = "RdYlBu"
    )

### Arguments

`tad_diff` | Raw object output by TADCompare. Required.
`cont_mat1` | contact matrix in either sparse 3 column, n x n or n x (n+3) form where the first three columns are coordinates in BED format. See "Input_Data" vignette for more information. If an x n matrix is used, the column names must correspond to the start point of the corresponding bin. Should correspond to the first contact matrix input into TADCompare. Required.
`cont_mat2` | contact matrix in either sparse 3 column, n x n or n x (n+3) form where the first three columns are coordinates in BED format. If an x n matrix is used, the column names must correspond to the start point of the corresponding bin. Should correspond to the second contact matrix input into TADCompare. Required.
`resolution` | Resolution of the data. Required.
`start_coord` | The start coordinate defining a region to plot. Required.
`end_coord` | The end coordinate defining a region to plot. Required.
`pre_tad` | A list of pre-defined TADs for drawing. Must contain two entries with the first corresponding to TADs detected in matrix 1 and the second to those detected in matrix 2. Each entry must contain a BED-like data frame or GenomicRanges object with columns "chr", "start", and "end", corresponding to coordinates of TADs. Must correspond to TADCompare results obtained for the same pre-defined TADs. Optional
`show_types` | If FALSE only the labels "Differential" and "Non-Differential" will be used. More in-depth differential boundary types will be excluded. Default is TRUE.
`point_size` | Parameter used to adjust the size of boundary points on heatmap plot. Default is 3.
`max_height` | Maximum height in bins that should be displayed on the heatmap plot. Default is 25.
`rel_heights` | Proportion of the size of the heatmap and score panels. Should be a vector containing the relative size of each panel with the heatmap panel coming first and the score panel second. Default is c(2, 1).
`palette` | Parameter used to adjust color palette. For list of palettes see https://rdrr.io/cran/RColorBrewer/man/ColorBrewer.html. Alternatively, users can define a vector of color names or hex codes. Default is 'RdYlBu'

### Details

Given a TADCompare object and two corresponding contact matrices, Diff_Plot provides visualization of user-specified regions of the genome with accompanying differential annotations, TAD scores and differential TAD scores

### Value

A ggplot plot containing a visualization of the upper diagonal both contact matrices with types of non-/differential boundaries labeled. The first matrix is shown on top and the second on the bottom. If pre_tad is provided, then the outline of the pre-defined TADs are shown. Individual TAD score and differential TAD scores are shown below the contact matrix plots.

### Examples

    # Read in data
    data("rao_chr22_prim")
    data("rao_chr22_rep")
    # Find differential TAD boundaries
    tad_diff <- TADCompare(rao_chr22_prim, rao_chr22_rep, resolution = 50000)
    # Create plot
    DiffPlot(tad_diff,rao_chr22_prim, rao_chr22_rep, resolution = 50000,
    start_coord = 22050000, end_coord = 24150000)

[Package TADCompare version 1.4.0 Index]