scale_region {lisaClust}R Documentation

Scale constructor for regions

Description

Region scale constructor.

Usage

scale_region(aesthetics = "region", ..., guide = "legend")

scale_region_manual(..., values)

Arguments

aesthetics

The names of the aesthetics that this scale works with

...

Arguments passed on to discrete_scale

guide

A function used to create a guide or its name. See guides() for more info.

values

a set of aesthetic values to map data values to. If this is a named vector, then the values will be matched based on the names. If unnamed, values will be matched in order (usually alphabetical) with the limits of the scale. Any data values that don't match will be given na.value.

Value

a ggplot guide

Examples


library(spicyR)
## Generate toy data
set.seed(51773)
x <- round(c(runif(200),runif(200)+1,runif(200)+2,runif(200)+3,
             runif(200)+3,runif(200)+2,runif(200)+1,runif(200)),4)*100
 y <- round(c(runif(200),runif(200)+1,runif(200)+2,runif(200)+3,
              runif(200),runif(200)+1,runif(200)+2,runif(200)+3),4)*100
cellType <- factor(paste('c',rep(rep(c(1:2),rep(200,2)),4),sep = ''))
imageID <- rep(c('s1', 's2'),c(800,800))
cells <- data.frame(x, y, cellType, imageID)

## Store data in SegmentedCells object
cellExp <- SegmentedCells(cells, cellTypeString = 'cellType')

## Generate LISA
lisaCurves <- lisa(cellExp)

## Cluster regions
kM <- kmeans(lisaCurves,2)
region(cellExp) <- paste('region',kM$cluster,sep = '_')

# Plot the regions with hatchingPlot()
hatchingPlot(cellExp) +
scale_region_manual(values = c(1,4), labels = c("Region A", "Region B"), 
name = "Regions")



[Package lisaClust version 1.0.0 Index]