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

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

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

sceObj <- BaronPancreasData('human')

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

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

## ----message=FALSE, warning=FALSE, results=FALSE------------------------------
seuratObj <- as.Seurat(sceObj)

## ----message=FALSE, warning=FALSE---------------------------------------------
mat1 <- scExpMat(sceObj)
dim(mat1)
mat2 <- scExpMat(seuratObj)
identical(mat1, mat2)

## -----------------------------------------------------------------------------
mat2 <- scExpMat(mat1)
identical(mat1, mat2)

## -----------------------------------------------------------------------------
is(mat1)[1]
mat2 <- scExpMat(sceObj, densify=FALSE)
is(mat2)[2]

## -----------------------------------------------------------------------------
mat2 <- scExpMat(sceObj, genes=rownames(sceObj)[seq(30, 80)])
dim(mat2)

## -----------------------------------------------------------------------------
col1 <- scCol(seuratObj, 'label')
col2 <- scCol(sceObj, 'label')
identical(col1, col2)
head(col1)

## -----------------------------------------------------------------------------
scCol(seuratObj, 'labelCopy') <- paste0(scCol(seuratObj, 'label'), '_copy')
head(seuratObj[['labelCopy']])

## -----------------------------------------------------------------------------
df1 <- metadataDF(seuratObj)
df2 <- metadataDF(sceObj)
identical(df1, df2)
head(df1)[, c(1, 2)]

## -----------------------------------------------------------------------------
colNames1 <- metadataNames(seuratObj)
colNames2 <- metadataNames(sceObj)
identical(colNames1, colNames2)
head(colNames1)

## -----------------------------------------------------------------------------
freq1 <- scColCounts(sceObj, 'donor')
freq2 <- scColCounts(seuratObj, 'donor')
identical(freq1, freq2)
head(freq1)
freq1 <- scColPairCounts(sceObj, 'donor', 'label')
freq2 <- scColPairCounts(seuratObj, 'donor', 'label')
identical(freq1, freq2)
head(freq1)

## -----------------------------------------------------------------------------
dimPlot(sceObj, groupBy='label')

## -----------------------------------------------------------------------------
featurePlot(sceObj, 'SOX4')

## -----------------------------------------------------------------------------
violinPlot(sceObj, 'SOX4', groupBy='label')

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