Plot cutpoints and densities for thresholding

# S3 method for thresholdSCRNACountMatrix
plot(x, ask = FALSE, wait.time = 0, type = "bin", indices = NULL, ...)

Arguments

x: output of thresholdSCRNACountMatrix
ask: if TRUE then will prompt before displaying each plot
wait.time: pause (in seconds) between each plot
type: one or more of the following: 'bin' (plot the genes by the binning used for thresholding), or 'gene' (plot thresholding by gene -- see next argument)
indices: if type is equal to 'gene', and is a integer of length 1, then a random sample of indices genes is taken. If it is NULL, then 10 genes are sampled. If it is a integer vector of length > 1, then it is interpreted as giving a list of indices of genes to be displayed.
...: further arguments passed to plot

Value

displays plots

Examples

## See thresholdSCRNACountMatrix
example(thresholdSCRNACountMatrix)
#> 
#> tSCRNA> data(maits,package='MAST', envir = environment())
#> 
#> tSCRNA> sca <- FromMatrix(t(maits$expressionmat[,1:1000]), maits$cdat, maits$fdat[1:1000,])
#> Assuming data assay in position 1, with name et is log-transformed.
#> 
#> tSCRNA> tt <- thresholdSCRNACountMatrix(assay(sca))
#> (0.0426,0.354]  (0.354,0.757]   (0.757,1.28]    (1.28,1.96]    (1.96,2.84] 
#>       2.258200       2.258200       2.258200       2.258200       2.258200 
#>    (2.84,3.99]    (3.99,13.2] 
#>       2.258200       3.313588 
#> 
#> tSCRNA> tt <- thresholdSCRNACountMatrix(2^assay(sca)-1, data_log=FALSE)
#> (0.0426,0.354]  (0.354,0.757]   (0.757,1.28]    (1.28,1.96]    (1.96,2.84] 
#>       2.258200       2.258200       2.258200       2.258200       2.258200 
#>    (2.84,3.99]    (3.99,13.2] 
#>       2.258200       3.313588 
#> 
#> tSCRNA> opar <- par(no.readonly = TRUE)
#> 
#> tSCRNA> on.exit(par(opar))
#> 
#> tSCRNA> par(mfrow=c(4,2))
#> 
#> tSCRNA> plot(tt)