## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup, eval=FALSE--------------------------------------------------------
# if (!require("BiocManager", quietly=TRUE))
#     install.packages("BiocManager")
# 
# BiocManager::install("hammers")

## ----message=FALSE, warning=FALSE, results=FALSE------------------------------
library(hammers)
library(scLang)
library(scRNAseq)
library(scater)

sceObj <- BaronPancreasData('human')

## ----message=FALSE, warning=FALSE, results=FALSE------------------------------
sceObj <- logNormCounts(sceObj)

## ----message=FALSE, warning=FALSE, results=FALSE------------------------------
sceObj <- runPCA(sceObj)
sceObj <- runUMAP(sceObj)

## -----------------------------------------------------------------------------
df <- genePresence(sceObj, rownames(sceObj)[seq(100)], 300, 2000)
dim(df)
head(df)

## -----------------------------------------------------------------------------
cellSets <- geneCellSets(sceObj, rownames(sceObj)[seq(100)])
head(cellSets[[1]])

## -----------------------------------------------------------------------------
df <- findRareGenes(sceObj, nCells=10)
dim(df)
head(df)

## ----message=FALSE, warning=FALSE---------------------------------------------
dim(sceObj)
sceObj <- removeRareGenes(sceObj, nCells=10)
dim(sceObj)

## -----------------------------------------------------------------------------
df <- repAnalysis(sceObj, 'donor', 'label')
head(df)
df <- repAnalysis(sceObj, 'donor', 'label', doOverrep=FALSE)
head(df)

## -----------------------------------------------------------------------------
pvalRiverPlot(df, title=NULL)

## -----------------------------------------------------------------------------
distributionPlot(sceObj, NULL, 'donor', 'label')

## -----------------------------------------------------------------------------
distributionPlot(sceObj, NULL, 'donor', 'label', type='percs')

## ----message=FALSE, warning=FALSE---------------------------------------------
genes <- c('PRSS1', 'TTR', 'GJD2', 'MS4A8')
geneCenters(sceObj, genes)

## ----message=FALSE, warning=FALSE---------------------------------------------
genesDimPlot(sceObj, genes, groupBy='label')

## ----message=FALSE, warning=FALSE---------------------------------------------
sceObj <- computeSilhouette(sceObj, 'label', 'labelSil')
head(scCol(sceObj, 'labelSil'))

## ----message=FALSE, warning=FALSE---------------------------------------------
df <- normalizeSilhouette(sceObj, 'label', 'labelSil')
head(df)

## ----message=FALSE, warning=FALSE---------------------------------------------
sceObj <- addNormSilhouette(sceObj, df, 'labelNormSil')
featurePlot(sceObj, 'labelNormSil')

## -----------------------------------------------------------------------------
sessionInfo()