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

## -----------------------------------------------------------------------------
library(scSorter)

## -----------------------------------------------------------------------------
load(url('https://github.com/hyguo2/scSorter/blob/master/inst/extdata/TMpancreas.RData?raw=true'))

## -----------------------------------------------------------------------------
expr[1:5, 1:5]
dim(expr)

## -----------------------------------------------------------------------------
head(anno)

## -----------------------------------------------------------------------------
topgenes = xfindvariable_genes(expr, ngenes = 2000)

## -----------------------------------------------------------------------------
expr = xnormalize_scData(expr)

## -----------------------------------------------------------------------------
topgene_filter = rowSums(as.matrix(expr)[topgenes, ]!=0) > ncol(expr)*.1
topgenes = topgenes[topgene_filter]

## -----------------------------------------------------------------------------
picked_genes = unique(c(anno$Marker, topgenes))
expr = expr[rownames(expr) %in% picked_genes, ]

## -----------------------------------------------------------------------------
#library(Seurat)
#expr_obj = CreateSeuratObject(expr)
#expr_obj <- NormalizeData(expr_obj, normalization.method = "LogNormalize", scale.factor = 10000, verbose = F)

## -----------------------------------------------------------------------------
#expr_obj <- FindVariableFeatures(expr_obj, selection.method = "vst", nfeatures = 2000, verbose = F)
#topgenes <- head(VariableFeatures(expr_obj), 2000)

#expr = GetAssayData(expr_obj)
#topgene_filter = rowSums(as.matrix(expr)[topgenes, ]!=0) > ncol(expr)*.1
#topgenes = topgenes[topgene_filter]

## -----------------------------------------------------------------------------
#picked_genes = unique(c(anno$Marker, topgenes))
#expr = expr[rownames(expr) %in% picked_genes, ]

## -----------------------------------------------------------------------------
rts <- scSorter(expr, anno)

## -----------------------------------------------------------------------------
print(table(rts$Pred_Type))

## -----------------------------------------------------------------------------
mis_rate = 1 - mean(rts$Pred_Type == true_type)
round(mis_rate, 4)

## -----------------------------------------------------------------------------
table(true_type, rts$Pred_Type)