params <- list(test = FALSE) ## ---- include = FALSE--------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) library(BiocStyle) ## ----warning=FALSE, message=FALSE--------------------------------------------- # load required packages library(spicyR) library(ggplot2) ## ---- eval = FALSE------------------------------------------------------------ # if (!require("BiocManager")) # install.packages("BiocManager") # BiocManager::install("spicyR") ## ----------------------------------------------------------------------------- data("diabetesData") diabetesData cellSummary(diabetesData) imagePheno(diabetesData) ## ----message=FALSE------------------------------------------------------------ spicyTestPair <- spicy(diabetesData, condition = "stage", subject = "case", from = "beta", to = "delta") spicyTestPair topPairs(spicyTestPair) ## ----eval=FALSE--------------------------------------------------------------- # spicyTest <- spicy(diabetesData, # condition = "stage", # subject = "case") ## ----------------------------------------------------------------------------- data("spicyTest") ## ----------------------------------------------------------------------------- spicyTest topPairs(spicyTest) ## ----------------------------------------------------------------------------- signifPlot(spicyTest, breaks=c(-3, 3, 0.5), marksToPlot = c("alpha", "beta", "gamma", "delta", "B", "naiveTc", "Th", "Tc", "neutrophil", "macrophage")) ## ----------------------------------------------------------------------------- data("spicyTestBootstrap") ## ----eval=FALSE, warning=FALSE, message=FALSE--------------------------------- # spicyTestBootstrap <- spicy(diabetesData, # condition = "stage", # subject = "case", # from = "beta", # to = "Tc", # nsim = 1000) ## ----------------------------------------------------------------------------- spicyTestBootstrap topPairs(spicyTestBootstrap) ## ----------------------------------------------------------------------------- sessionInfo()