Plots Aggregate Peak Analysis Matrix

Plots Aggregate Peak Analysis Matrix

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")
#> Error in pgParams(width = 3, height = 3, default.units = "inches"): could not find function "pgParams"

## Create page
pageCreate(params = p)
#> Error in pageCreate(params = p): could not find function "pageCreate"

## 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)
#> Error in eval(expr, p): object 'p' not found

## Annotate legend
annoHeatmapLegend(plot = plot,
                  x = 2.3, y = 0.75, width = 0.1, height = 0.75)
#> Error in annoHeatmapLegend(plot = plot, x = 2.3, y = 0.75, width = 0.1,     height = 0.75): could not find function "annoHeatmapLegend"


## 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")
#> Error in pgParams(width = 3, height = 3, default.units = "inches"): could not find function "pgParams"

## Create page
pageCreate(params = p)
#> Error in pageCreate(params = p): could not find function "pageCreate"

## 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)
#> Error in eval(expr, p): object 'p' not found

## Annotate legend
annoHeatmapLegend(plot = plot,
                  x = 2.3, y = 0.75, width = 0.1, height = 0.75)
#> Error in annoHeatmapLegend(plot = plot, x = 2.3, y = 0.75, width = 0.1,     height = 0.75): could not find function "annoHeatmapLegend"