View source: R/MakeSigMatrix.R
plotKappas | R Documentation |
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))
plotKappas( kappas, nGenes, smData = NULL, titleStr = "Shrink Signature Matrix", bonusPoints = NULL, maxCond = 100 )
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) |
a matrix including imputed values
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)
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