@@ -4,3 +4,4 @@

 ^Meta$

 ^\.vscode$

 ^_pkgdown\.yml$

+^\.github$

new file mode 100644

@@ -0,0 +1 @@

+*.html

new file mode 100644

@@ -0,0 +1,50 @@

+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples

+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help

+on:

+  push:

+    branches: [devel, master]

+  pull_request:

+    branches: [devel, master]

+  release:

+    types: [published]

+  workflow_dispatch:

+

+name: pkgdown.yaml

+

+permissions: read-all

+

+jobs:

+  pkgdown:

+    runs-on: ubuntu-latest

+    # Only restrict concurrency for non-PR jobs

+    concurrency:

+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}

+    env:

+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

+    permissions:

+      contents: write

+    steps:

+      - uses: actions/checkout@v4

+

+      - uses: r-lib/actions/setup-pandoc@v2

+

+      - uses: r-lib/actions/setup-r@v2

+        with:

+          use-public-rspm: true

+

+      - uses: r-lib/actions/setup-r-dependencies@v2

+        with:

+          extra-packages: any::pkgdown, local::.

+          needs: website

+

+      - name: Build site

+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)

+        shell: Rscript {0}

+

+      - name: Deploy to GitHub pages 🚀

+        if: github.event_name != 'pull_request'

+        uses: JamesIves/[email protected]

+        with:

+          clean: false

+          branch: gh-pages

+          folder: docs

@@ -1,7 +1,7 @@

 Package: lisaClust

 Type: Package

 Title: lisaClust: Clustering of Local Indicators of Spatial Association

-Version: 1.12.2

+Version: 1.12.3

 Authors@R: c(

     person("Ellis", "Patrick", , "[email protected]", role = c("aut", "cre")),

     person("Nicolas", "Canete", , "[email protected]", role = "aut"),

@@ -42,5 +42,5 @@ Imports:

     SummarizedExperiment,

     pheatmap,

     spatstat.random

-Suggests: BiocStyle, knitr, rmarkdown

+Suggests: BiocStyle, knitr, rmarkdown, SpatialDatasets

 RoxygenNote: 7.3.1

@@ -32,6 +32,7 @@

 #' cellType <- factor(paste("c", rep(rep(c(1:2), rep(200, 2)), 4), sep = ""))

 #' imageID <- rep(c("s1", "s2"), c(800, 800))

 #' cells <- data.frame(x, y, cellType, imageID)

+#' cells <- SingleCellExperiment::SingleCellExperiment(colData = cells)

 #'

 #' ## Generate regions

 #' cells <- lisaClust(cells, k = 2)

@@ -239,6 +240,7 @@ geom_hatching <-

 #' cellType <- factor(paste("c", rep(rep(c(1:2), rep(200, 2)), 4), sep = ""))

 #' imageID <- rep(c("s1", "s2"), c(800, 800))

 #' cells <- data.frame(x, y, cellType, imageID)

+#' cells <- SingleCellExperiment::SingleCellExperiment(colData = cells)

 #'

 #' ## Generate regions

 #' cells <- lisaClust(cells, k = 2)

@@ -120,6 +120,7 @@ y <- round(c(

 cellType <- factor(paste("c", rep(rep(c(1:2), rep(200, 2)), 4), sep = ""))

 imageID <- rep(c("s1", "s2"), c(800, 800))

 cells <- data.frame(x, y, cellType, imageID)

+cells <- SingleCellExperiment::SingleCellExperiment(colData = cells)

 ## Generate regions

 cells <- lisaClust(cells, k = 2)

@@ -43,6 +43,7 @@ y <- round(c(

 cellType <- factor(paste("c", rep(rep(c(1:2), rep(200, 2)), 4), sep = ""))

 imageID <- rep(c("s1", "s2"), c(800, 800))

 cells <- data.frame(x, y, cellType, imageID)

+cells <- SingleCellExperiment::SingleCellExperiment(colData = cells)

 ## Generate regions

 cells <- lisaClust(cells, k = 2)

@@ -46,10 +46,8 @@ BiocManager::install("lisaClust")

 ```{r message=FALSE, warning=FALSE}

 # load required packages

-# library(lisaClust)

-# library(spicyR)

-devtools::load_all("~/spicyR")

-devtools::load_all("/dskh/nobackup/alexq/lisaClust")

+library(lisaClust)

+library(spicyR)

 library(ggplot2)

 library(SingleCellExperiment)

 library(SpatialDatasets)