plotApa: Plots Aggregate Peak Analysis Matrix

In EricSDavis/hictoolsr: An R Package for Hi-C Data Analysis

Plots Aggregate Peak Analysis Matrix

Description

Plots Aggregate Peak Analysis Matrix

Usage

plotApa(
  params = NULL,
  apa,
  x = NULL,
  y = NULL,
  width = NULL,
  height = NULL,
  just = c("left", "top"),
  default.units = "inches",
  draw = TRUE,
  palette = colorRampPalette(c("white", "dark red")),
  n = NULL,
  zrange = NULL
)

Arguments

params	optional "pgParams" object containing relevant function parameters
x	numeric or unit object specifying x-location of plot
y	numeric or unit object specifying y-location of plot
width	numeric or unit object specifying width of plot
height	numeric or unit object specifying height of plot
just	string or numeric vector specifying the justification of the viewport relative to its (x, y) location
default.units	string indicating the default units to use if x, y, width, or height are only given as numeric vectors
draw	logical value indicating whether graphics output should be produced
palette	colorRampPalette function to use to map values to colors
n	numeric by which to divide aggregate matrix
zrange	vector of length 2; max and min values to set color scale
data	matrix, list of matricies, or 3 column data.frame of APA results

Value

Function will draw a APA matrix and return an object of class "apa"

Examples

## Create divergent matrix ####
m <- matrix(data = rnorm(n = 21*21, mean = 0, sd = 2), nrow = 21, ncol = 21)

## Define parameters
p <- pgParams(width = 3, height = 3, default.units = "inches")

## Create page
pageCreate(params = p)

## Plot apa
plot <- plotApa(apa = m,
                x = p$width/2, y = p$height/2,
                width = p$width*0.5, height = p$width*0.5, just = c("center", "center"),
                palette = colorRampPalette(c("blue", "white", "red")), zrange = NULL)

## Annotate legend
annoHeatmapLegend(plot = plot,
                  x = 2.3, y = 0.75, width = 0.1, height = 0.75)


## Create sequential matrix
m <- matrix(data = sample(0:100, 21*21, replace = T), nrow = 21, ncol = 21)

## Define parameters
p <- pgParams(width = 3, height = 3, default.units = "inches")

## Create page
pageCreate(params = p)

## Plot apa
plot <- plotApa(apa = m,
                x = p$width/2, y = p$height/2,
                width = p$width*0.5, height = p$width*0.5, just = c("center", "center"),
                palette = colorRampPalette(c("white", "dark red")), zrange = NULL)

## Annotate legend
annoHeatmapLegend(plot = plot,
                  x = 2.3, y = 0.75, width = 0.1, height = 0.75)

EricSDavis/hictoolsr documentation built on Sept. 4, 2022, 12:36 a.m.