Plot matrix

Used to plot single or aggregate matrix such as aggregate peak analysis.

Usage

plotMatrix(
  data,
  params = NULL,
  x = NULL,
  y = NULL,
  width = NULL,
  height = NULL,
  just = c("left", "top"),
  default.units = "inches",
  draw = TRUE,
  palette = colorRampPalette(RColorBrewer::brewer.pal(9, "YlGnBu")),
  zrange = NULL,
  na.color = "grey"
)

# S4 method for DelayedMatrix_OR_matrix
plotMatrix(
  data,
  params = NULL,
  x = NULL,
  y = NULL,
  width = NULL,
  height = NULL,
  just = c("left", "top"),
  default.units = "inches",
  draw = TRUE,
  palette = colorRampPalette(RColorBrewer::brewer.pal(9, "YlGnBu")),
  zrange = NULL,
  na.color = "grey"
)

Arguments

data

`DelayedMatrix`, `matrix`, list of matrices, or 3 column `data.frame` of APA results.

params

Optional `pgParams` object containing relevant function parameters.

x

Numeric or unit object specifying the x-location of plot.

y

Numeric or unit object specifying the y-location of plot.

width

Numeric or unit object specifying the width of plot.

height

Numeric or unit object specifying the 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 for mapping values to colors.

zrange

Vector of length 2; max and min values to set color scale

na.color

String indicating the color to use for mapping NA values.

Value

Function will draw a color-mapped matrix and return an S3 object of class `MatrixPlot`.

Examples

library(plotgardener)
#> 
#> Attaching package: ‘plotgardener’
#> The following object is masked from ‘package:base’:
#> 
#>     c
library(RColorBrewer)

## 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 <- plotMatrix(data=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)
#> MatrixPlot[MatrixPlot1]

## Annotate legend
annoHeatmapLegend(plot=plot,
                  x=2.3,
                  y=0.75,
                  width=0.1,
                  height=0.75)
#> heatmapLegend[heatmapLegend1]



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

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

## Create page
pageCreate(params=p)

## Plot apa
plot <- plotMatrix(data=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)
#> MatrixPlot[MatrixPlot1]

## Annotate legend
annoHeatmapLegend(plot=plot,
                  x=2.3,
                  y=0.75,
                  width=0.1,
                  height=0.75)
#> heatmapLegend[heatmapLegend1]