plotKappas {ADAPTS}R Documentation

Plot condition numbers

Description

Plot the condition numbers during the growing and shrinking of signature matrices.

bonusPoints <- data.frame(legText = c('Unagumented Signature Matrix', 'Minimum Smoothed Condition Number', 'Best Augmented Signature Matrix'), pchs = c('o', 'x', 'x'), cols = c('red', 'purple', 'blue'), kappa = c(10, 15, 20), nGene = c(5, 10, 15))

Usage

plotKappas(
  kappas,
  nGenes,
  smData = NULL,
  titleStr = "Shrink Signature Matrix",
  bonusPoints = NULL,
  maxCond = 100
)

Arguments

kappas

The condition numbers to plot

nGenes

The number of genes associated with each kapp

smData

Smoothed data to plot as a green line (DEFAULT: NULL)

titleStr

The title of the plot (DEFAULT: 'Shrink Signature Matrix')

bonusPoints

Set to plot additional points on the plot, see description (DEFAULT: NULL)

maxCond

Cap the condition number to maxCond (DEFAULT: 100)

Value

a matrix including imputed values

Examples

nGenes <- 1:300
kappas <- log(abs(nGenes-250))
kappas[is.infinite(kappas)] <- 0
kappas <- kappas+runif(300, 0, 1)
smData <- stats::smooth(kappas)
bonusPoints <- data.frame(legText = 'Minimum Smoothed ', pchs='x', cols='purple', 
kappa=min(smData), nGenes=nGenes[which.min(smData)])
plotKappas(kappas=kappas, nGenes=nGenes, smData=smData, bonusPoints=bonusPoints, maxCond=100)


[Package ADAPTS version 1.0.6 Index]