update docs

.github/workflows/rworkflows.yml

@@ -0,0 +1,57 @@
+name: rworkflows
+'on':
+  push:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+  pull_request:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+jobs:
+  rworkflows:
+    permissions: write-all
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    strategy:
+      fail-fast: ${{ false }}
+      matrix:
+        config:
+        - os: ubuntu-latest
+          bioc: devel
+          r: auto
+          cont: ghcr.io/bioconductor/bioconductor_docker:devel
+          rspm: ~
+        - os: macOS-latest
+          bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+        - os: windows-latest
+          bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+    steps:
+    - uses: neurogenomics/rworkflows@master
+      with:
+        run_bioccheck: ${{ false }}
+        run_rcmdcheck: ${{ true }}
+        as_cran: ${{ true }}
+        run_vignettes: ${{ true }}
+        has_testthat: ${{ true }}
+        run_covr: ${{ true }}
+        run_pkgdown: ${{ true }}
+        has_runit: ${{ false }}
+        has_latex: ${{ false }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run_docker: ${{ false }}
+        DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
+        runner_os: ${{ runner.os }}
+        cache_version: cache-v1
+        docker_registry: ghcr.io

.gitignore

@@ -3,3 +3,4 @@ inst/doc
 vignettes/*.html
 vignettes/*.R
 docs
+README.html

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ggsc
 Title: Visualizing Single Cell Data
-Version: 1.1.1.002
+Version: 1.1.1.003
 Authors@R: c(
        person("Guangchuang", "Yu", 
               email = "[email protected]", 
@@ -60,7 +60,7 @@ Suggests:
   STexampleData,
   testthat (>= 3.0.0)
 BugReports: https://github.com/YuLab-SMU/ggsc/issues 
-URL: https://github.com/YuLab-SMU/ggsc
+URL: https://github.com/YuLab-SMU/ggsc (devel), https://yulab-smu.top/ggsc/ (docs)
 biocViews: DimensionReduction, GeneExpression, SingleCell, 
   Software, Spatial, Transcriptomics,Visualization
 VignetteBuilder: knitr

NEWS.md

@@ -1,5 +1,8 @@
-# ggsc 1.1.1.002
+# ggsc 1.1.1.003
 
++ add `sc_dot()` method for 'Seurat' object (2023-11-29, Wed, #15)
++ update vignette to link to the online docs (<https://yulab-smu.top/ggsc>)
++ add `README.Rmd` and `README.md` in github repo
 + optimization: retrieve embedding without `FetchData` (2023-11-27, Mon, #14)
 + bug fixed for Seurat object (2023-10-31, Tue, #12, #13)
 
@@ -44,4 +47,10 @@
 
 # scplot 0.0.1
 
-+ `sc_dim`, `sc_dim_geom_feature`, `sc_dim_geom_label`, `sc_feature`, `sc_geom_point` and `sc_violin` functions (2022-11-09, Wed)
++ several functions implemented (2022-11-09, Wed)
+    - `sc_dim`
+    - `sc_dim_geom_feature`
+    - `sc_dim_geom_label`
+    - `sc_feature`
+    - `sc_geom_point`
+    - `sc_violin`

README.Rmd

@@ -0,0 +1,73 @@
+---
+title: "`r read.dcf('DESCRIPTION', fields = 'Package')[1]`"  
+date: "<h4>README updated: <i>`r format( Sys.Date())`</i></h4>"
+output:
+  github_document
+html_preview: false
+---
+
+
+
+<!-- generated by rworkflows::use_readme() -->
+
+[![License: Artistic-2.0](https://img.shields.io/badge/license-Artistic--2.0-blue.svg)](https://cran.r-project.org/web/licenses/Artistic-2.0)
+[![](https://img.shields.io/badge/devel%20version-1.1.1.002-black.svg)](https://github.com/YuLab-SMU/ggsc)
+[![](https://img.shields.io/github/languages/code-size/YuLab-SMU/ggsc.svg)](https://github.com/YuLab-SMU/ggsc)
+[![](https://img.shields.io/github/last-commit/YuLab-SMU/ggsc.svg)](https://github.com/YuLab-SMU/ggsc/commits/master)
+<br>
+[![R build status](https://github.com/YuLab-SMU/ggsc/workflows/rworkflows/badge.svg)](https://github.com/YuLab-SMU/ggsc/actions)
+[![](https://codecov.io/gh/YuLab-SMU/ggsc/branch/master/graph/badge.svg)](https://app.codecov.io/gh/YuLab-SMU/ggsc)
+<br>
+<a href="https://app.codecov.io/gh/YuLab-SMU/ggsc/tree/master" target='_blank'><img src="https://codecov.io/gh/YuLab-SMU/ggsc/branch/master/graphs/icicle.svg" title="Codecov icicle graph" width="200" height="50" style="vertical-align: top;"></a>
+
+
+<!-- To modify Package/Title/Description/Authors fields, edit the DESCRIPTION file -->
+
+```{r, echo=FALSE, include=FALSE}
+pkg <- read.dcf("DESCRIPTION", fields = "Package")[1]
+title <- read.dcf("DESCRIPTION", fields = "Title")[1]
+description <- read.dcf("DESCRIPTION", fields = "Description")[1]
+description <- gsub("\n", " ", description)
+URL <- read.dcf('DESCRIPTION', fields = 'URL')[1]
+owner <- tolower(strsplit(URL,"/")[[1]][4])
+```
+
+
+## ``r pkg``: `r title`
+
+### `r description`
+
+
+## :writing_hand: Authors
+
+Guangchuang YU 
+
+School of Basic Medical Sciences, Southern Medical University
+
+<https://yulab-smu.top>
+
+
+<!-- 
+If you use ``r pkg``, please cite: -->
+
+<!-- Modify this by editing the file: inst/CITATION  -->
+
+<!-- 
+> `r utils::citation(pkg)$textVersion`
+-->
+
+
+## :arrow_double_down: Installation 
+
+```R
+if(!require("remotes")) install.packages("remotes")
+
+remotes::install_github("`r URL`")
+library(`r pkg`)
+```
+## Documentation 
+
+### [Website](https://yulab-smu.top/ggsc)
+
+
+<br>

README.md

@@ -0,0 +1,54 @@
+ggsc
+================
+<h4>  
+README updated: <i>2023-11-29</i>  
+</h4>
+
+<!-- generated by rworkflows::use_readme() -->
+
+[![License:
+Artistic-2.0](https://img.shields.io/badge/license-Artistic--2.0-blue.svg)](https://cran.r-project.org/web/licenses/Artistic-2.0)
+[![](https://img.shields.io/badge/devel%20version-1.1.1.002-black.svg)](https://github.com/YuLab-SMU/ggsc)
+[![](https://img.shields.io/github/languages/code-size/YuLab-SMU/ggsc.svg)](https://github.com/YuLab-SMU/ggsc)
+[![](https://img.shields.io/github/last-commit/YuLab-SMU/ggsc.svg)](https://github.com/YuLab-SMU/ggsc/commits/master)
+<br> [![R build
+status](https://github.com/YuLab-SMU/ggsc/workflows/rworkflows/badge.svg)](https://github.com/YuLab-SMU/ggsc/actions)
+[![](https://codecov.io/gh/YuLab-SMU/ggsc/branch/master/graph/badge.svg)](https://app.codecov.io/gh/YuLab-SMU/ggsc)
+<br>
+<a href="https://app.codecov.io/gh/YuLab-SMU/ggsc/tree/master" target='_blank'><img src="https://codecov.io/gh/YuLab-SMU/ggsc/branch/master/graphs/icicle.svg" title="Codecov icicle graph" width="200" height="50" style="vertical-align: top;"></a>
+
+<!-- To modify Package/Title/Description/Authors fields, edit the DESCRIPTION file -->
+
+## `ggsc`: Visualizing Single Cell Data
+
+### Useful functions to visualize single cell and spatial data. It supports both ‘SingleCellExperiment’ and ‘Seurat’ objects. It also supports visualizing the data using grammar of graphics implemented in ‘ggplot2’.
+
+## :writing_hand: Authors
+
+Guangchuang YU
+
+School of Basic Medical Sciences, Southern Medical University
+
+<https://yulab-smu.top>
+
+<!-- 
+If you use `ggsc`, please cite: -->
+<!-- Modify this by editing the file: inst/CITATION  -->
+<!-- 
+> 
+-->
+
+## :arrow_double_down: Installation
+
+``` r
+if(!require("remotes")) install.packages("remotes")
+
+remotes::install_github("https://github.com/YuLab-SMU/ggsc (devel), https://yulab-smu.top/ggsc/ (docs)")
+library(ggsc)
+```
+
+## Documentation
+
+### [Website](https://yulab-smu.top/ggsc)
+
+<br>