## ----------------------------------------------------------------------------- library(Sconify) wand.final$IL7.fraction.cond.2[1:10] knitr::opts_chunk$set(fig.width=6, fig.height=4) ## ----------------------------------------------------------------------------- # Visualization MakeHist(wand.final, 30, "IL7.fraction.cond.2", "fraction IL7") # Characteristics of the visualization median(wand.final$IL7.fraction.cond.2) sd(wand.final$IL7.fraction.cond.2) ## ----------------------------------------------------------------------------- # Compare to a coin toss distribution # Flips a coin k number of times, n repetitions, and returns the vector # containing the per-k percent heads KFlip <- function(k, n) { # The result result <- sapply(1:n, function(i) { # Get the fraction heads for n flips flips <- sample(c(0, 1), k, replace = TRUE) percent.heads <- sum(flips)/length(flips) return(percent.heads) }) } coin.toss <- data.frame("binomial" = KFlip(30, 1000)) MakeHist(coin.toss, 30, "binomial", "fraction heads") median(coin.toss$binomial) sd(coin.toss$binomial) ## ----------------------------------------------------------------------------- # Raw per-cell IgM levels TsneVis(wand.final, "IgM(Eu153)Di", "Raw IgM expression") TsneVis(wand.final, "IL7.fraction.cond.2", "Fraction cells in Il7 condition") ## ----------------------------------------------------------------------------- # Before normalization MakeHist(bz.gmcsf.final, 100, "fraction.cond2", "fraction GM-CSF") # Characteristics of the visualization median(bz.gmcsf.final$fraction.cond2) sd(bz.gmcsf.final$fraction.cond2) # After normalization MakeHist(bz.gmcsf.final.norm.scale, 100, "fraction.cond2", "fraction GM-CSF") # Characteristics of the visualization median(bz.gmcsf.final.norm.scale$fraction.cond2) sd(bz.gmcsf.final.norm.scale$fraction.cond2) ## ----------------------------------------------------------------------------- # t-SNE map colored by KNN-based fraction GM-CSF TsneVis(bz.gmcsf.final, "fraction.cond2", "Fraction GM-CSF") # t-SNE map colored by KNN-based fraction GM-CSF TsneVis(bz.gmcsf.final.norm.scale, "fraction.cond2", "Fraction GM-CSF")