DiffPlot: Visualization of differential TAD boundaries

In cresswellkg/TADCompare: TADCompare: Identification and characterization of differential TADs

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)

cresswellkg/TADCompare documentation built on Dec. 1, 2020, 10:35 p.m.