update docs and change doc site deploy way

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# 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: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+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@v3
+
+      - 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

.gitignore

@@ -28,3 +28,4 @@ inst/extdata/COSMIC_v3.4_SBS_GRCh37.rds
 inst/extdata/COSMIC_v3.4_SV_GRCh38.rds
 inst/extdata/human_T2T_gene_info.rds
 inst/extdata/ce11_gene_info.rds
+docs

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: sigminer
 Title: Extract, Analyze and Visualize Mutational Signatures for Genomic
     Variations
-Version: 2.2.2
+Version: 2.3.0
 Authors@R: c(
     person("Shixiang", "Wang", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-9855-7357")),
@@ -26,7 +26,7 @@ Description: Genomic alterations including single nucleotide substitution,
     extract, analyze and visualize signatures from genomic alteration
     records, thus providing new insight into cancer study.
 License: MIT + file LICENSE
-URL: https://github.com/ShixiangWang/sigminer
+URL: https://github.com/ShixiangWang/sigminer, https://shixiangwang.github.io/sigminer/, https://shixiangwang.github.io/sigminer-book/
 BugReports: https://github.com/ShixiangWang/sigminer/issues
 Depends: 
     R (>= 3.5)

R/data.R

@@ -19,6 +19,15 @@ NULL
 #' data(centromeres.hg38)
 NULL
 
+#' Location of Centromeres at Genome Build T2T
+#' @docType data
+#' @name centromeres.T2T
+#' @format A data.frame
+#' @source from T2T study
+#' @examples
+#' data(centromeres.T2T)
+NULL
+
 #' Location of Centromeres at Genome Build mm10
 #' @docType data
 #' @name centromeres.mm10
@@ -62,6 +71,15 @@ NULL
 #' data(chromsize.hg38)
 NULL
 
+#' Chromosome Size of Genome Build T2T
+#' @docType data
+#' @name chromsize.T2T
+#' @format A data.frame
+#' @source from T2T study
+#' @examples
+#' data(chromsize.T2T)
+NULL
+
 #' Chromosome Size of Genome Build mm10
 #' @docType data
 #' @name chromsize.mm10
@@ -96,6 +114,15 @@ NULL
 #' data(cytobands.hg38)
 NULL
 
+#' Location of Chromosome Cytobands at Genome Build T2T
+#' @docType data
+#' @name cytobands.T2T
+#' @format A data.frame
+#' @source from T2T study
+#' @examples
+#' data(cytobands.T2T)
+NULL
+
 #' Location of Chromosome Cytobands at Genome Build mm10
 #' @docType data
 #' @name cytobands.mm10
@@ -130,6 +157,15 @@ NULL
 #' data(transcript.hg38)
 NULL
 
+#' Merged Transcript Location at Genome Build T2T
+#' @docType data
+#' @name transcript.T2T
+#' @format A `data.table`
+#' @source from T2T study.
+#' @examples
+#' data(transcript.T2T)
+NULL
+
 #' Merged Transcript Location at Genome Build mm10
 #' @docType data
 #' @name transcript.mm10

_pkgdown.yml

@@ -9,9 +9,6 @@ template:
     primary: "#0054AD"
     border-radius: 0.5rem
     btn-border-radius: 0.25rem
-  # params:
-  #   bootswatch: united
-destination: docs
 
 authors:
   Shixiang Wang:
@@ -126,18 +123,22 @@ reference:
     - CN.features
     - centromeres.hg19
     - centromeres.hg38
+    - centromeres.T2T
     - centromeres.mm10
     - centromeres.mm9
     - chromsize.hg19
     - chromsize.hg38
+    - chromsize.T2T
     - chromsize.mm10
-    - - chromsize.mm9
+    - chromsize.mm9
     - cytobands.hg19
     - cytobands.hg38
+    - cytobands.T2T
     - cytobands.mm10
     - cytobands.mm9
     - transcript.hg19
     - transcript.hg38
+    - transcript.T2T
     - transcript.mm10
     - transcript.mm9
   - title: Helpers