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) library(SingleCellExperiment) ## ---- eval = FALSE------------------------------------------------------------ # if (!require("BiocManager")) { # install.packages("BiocManager") # } # BiocManager::install("spicyR") ## ----------------------------------------------------------------------------- data("diabetesData_SCE") diabetesData_SCE ## ----message=FALSE------------------------------------------------------------ spicyTestPair <- spicy( diabetesData_SCE, condition = "stage", subject = "case", from = "beta", to = "delta" ) topPairs(spicyTestPair) ## ----message=FALSE------------------------------------------------------------ spicyTest <- spicy( diabetesData_SCE, condition = "stage", subject = "case" ) spicyTest topPairs(spicyTest) ## ----------------------------------------------------------------------------- signifPlot( spicyTest, breaks = c(-3, 3, 1), marksToPlot = c( "alpha", "beta", "gamma", "delta", "B", "naiveTc", "Th", "Tc", "neutrophil", "macrophage" ) ) ## ----------------------------------------------------------------------------- sessionInfo()