## ----global_options, include=FALSE--------------------------------------------
knitr::opts_chunk$set(warning=FALSE, message=FALSE, include = TRUE,
                        fig.height = 8, fig.width = 8, fig.align = "center",
                        echo=TRUE
                        )


## ----install, eval = FALSE----------------------------------------------------
#  
#  BiocManager::install('Spaniel')
#  
#  

## ---- load libraries----------------------------------------------------------
library(Spaniel)
library(DropletUtils)
library(scater)
library(scran)


## ----counts-------------------------------------------------------------------
pathToTenXOuts <- file.path(system.file(package = "Spaniel"), "extdata/outs")

sce <- createVisiumSCE(tenXDir=pathToTenXOuts, 
                            resolution="Low")


## ----barcodes-----------------------------------------------------------------
colData(sce)[, c("Barcode", "pixel_x", "pixel_y")]

## ----image_dimensions---------------------------------------------------------
metadata(sce)$ImgDims

## ----grob---------------------------------------------------------------------
metadata(sce)$Grob

## ---- qcplotting,  results = "hide"-------------------------------------------

filter <- sce$detected > 0
spanielPlot(object = sce,
        plotType = "NoGenes", 
        showFilter = filter, 
        techType = "Visium", 
        ptSizeMax = 3)




## -----------------------------------------------------------------------------
sce <- sce[, filter]

## ---- gene plot,  results = "hide"--------------------------------------------


sce <- logNormCounts(sce)

gene <- "ENSMUSG00000024843"
p2 <- spanielPlot(object = sce,
        plotType = "Gene", 
        gene = "ENSMUSG00000024843",
        techType = "Visium", 
        ptSizeMax = 3)

p2


## -----------------------------------------------------------------------------
library(scran)
sce <- logNormCounts(sce)
sce <- runPCA(sce)
sce <- runUMAP(sce)
g <- buildSNNGraph(sce, k = 70)

clust <- igraph::cluster_walktrap(g)$membership
sce$clust <- factor(clust)

## -----------------------------------------------------------------------------

p3 <- plotReducedDim(sce, "UMAP", colour_by="clust") 
p3

## -----------------------------------------------------------------------------
p4 <- spanielPlot(object = sce,
        plotType = "Cluster", 
        clusterRes = "clust",
        showFilter = NULL, 
        techType = "Visium", 
        ptSizeMax = 1, customTitle = "Section A")  

p4