## ----set up, include = FALSE-------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----setup, message = FALSE, warning=FALSE------------------------------------ library(stJoincount) library(pheatmap) library(ggplot2) ## ----"install", eval = FALSE-------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) { # install.packages("BiocManager") # } # BiocManager::install("stJoincount") ## ----------------------------------------------------------------------------- fpath <- system.file("extdata", "dataframe.rda", package="stJoincount") load(fpath) head(humanBC) ## ----------------------------------------------------------------------------- fpath <- system.file("extdata", "SeuratBC.rda", package="stJoincount") load(fpath) df <- dataPrepFromSeurat(seuratBC, "label") ## ----------------------------------------------------------------------------- fpath <- system.file("extdata", "SpeBC.rda", package="stJoincount") load(fpath) df2 <- dataPrepFromSpE(SpeObjBC, "label") ## ----------------------------------------------------------------------------- resolutionList <- resolutionCalc(humanBC) resolutionList ## ----------------------------------------------------------------------------- mosaicIntegration <- rasterizeEachCluster(humanBC) ## ----fig.dim = c(6, 6)-------------------------------------------------------- mosaicIntPlot(humanBC, mosaicIntegration) ## ----------------------------------------------------------------------------- joincount.result <- joincountAnalysis(mosaicIntegration) ## ----fig.dim = c(6, 6)-------------------------------------------------------- matrix <- zscoreMatrix(humanBC, joincount.result) zscorePlot(matrix) ## ----------------------------------------------------------------------------- sessionInfo()