## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE, results = "markup", message = FALSE, warning = FALSE) knitr::opts_chunk$set(fig.width=6, fig.height=4) ## ----------------------------------------------------------------------------- library(Sconify) wand.final <- PostProcessing(scone.output = wand.scone, cell.data = wand.combined, input = input.markers) wand.combined # input data wand.scone # scone-generated data wand.final # the data after post-processing # tSNE map shows highly responsive population of interest TsneVis(wand.final, "pSTAT5(Nd150)Di.IL7.change", "IL7 -> pSTAT5 change") # tSNE map now colored by q value TsneVis(wand.final, "pSTAT5(Nd150)Di.IL7.qvalue", "IL7 -> pSTAT5 -log10(qvalue)") # tSNE map colored by KNN density estimation TsneVis(wand.final, "density") ## ----------------------------------------------------------------------------- wand.final.sub <- SubsampleAndTsne(dat = wand.final, input = input.markers, numcells = 500) wand.final.sub