Update R docs and doc-site

api/r/cellxgene.census/README.md

@@ -1,39 +1,86 @@
 
-# CZ CELLxGENE Discover Census
+# R package of CZ CELLxGENE Discover Census
 
 <!-- badges: start -->
 <!-- badges: end -->
 
+This is the documentation for the R package `cellxgene.census` which is part of CZ CELLxGENE Discover Census. For full details on Census data and capabilities please go to the [main Census site](https://chanzuckerberg.github.io/cellxgene-census/).  
 
-The `cellxgene.census` package provides an API to facilitate the use of the CZ CELLxGENE Discover Census. For more information about the API and the project visit the [chanzuckerberg/cellxgene-census GitHub repo](https://github.com/chanzuckerberg/cellxgene-census/).
+`cellxgene.census` provides an API to efficiently access the cloud-hosted Census single-cell data from R. In just a few seconds users can access any slice of Census data using cell or gene filters across hundreds of single-cell datasets. 
 
-**Status**: Pre-release, under rapid development. Expect API changes.
-
-Also see the [Python API](https://cellxgene-census.readthedocs.io/).
+Census data can be fetched in an iterative fashion for bigger-than-memory slices of data, or quickly exported to basic R structures, as well as `Seurat` or `SingleCellExperiment` objects for downstream analysis.
 
 ## Installation
 
-You can install the development version of `cellxgene.census` from [GitHub](https://github.com/) with:
+From an R session, first install `tiledb` from R-Universe, as the latest release in CRAN is not yet available.
+
+```r
+install.packages(
+  "tiledb",
+  version = "0.20.2", 
+  repos=c('https://tiledb-inc.r-universe.dev','https://cloud.r-project.org') 
+)
+```
+
+Then install `cellxgene.census` from R-Universe.
 
-``` r
-# install.packages("devtools")
-devtools::install_github("chanzuckerberg/cellxgene-census/api/r/cellxgene.census")
-print(cellxgene.census::open_soma())
+```r
+install.packages(
+  "cellxgene.census",
+  repos=c('https://tiledb-inc.r-universe.dev','https://cloud.r-project.org') 
+)
 ```
 
-(minimal apt dependencies: r-base cmake git)
+## Usage
+
+Check out the vignettes in the "Articles" section of the navigation bar on this site. We highly recommend the following vignettes as a starting point:
+
+* [Querying and fetching the single-cell data and cell/gene metadata](./articles/census_query_extract.html)
+* [Learning about the CZ CELLxGENE Discover Census](./articles/comp_bio_census_info.html)
+
+You can also check out out the [quick start guide](https://chanzuckerberg.github.io/cellxgene-census/cellxgene_census_docsite_quick_start.html) in the main Census site.
+
+
+### Example `Seurat` and `SingleCellExperiment` query
+
+The following creates a `Seurat` object on-demand with all sympathetic neurons in Census and filtering only for the genes `ENSG00000161798`, `ENSG00000188229`.
+
+```r
+library("cellxgene.census")
+library("Seurat")
+
+census <- open_soma()
+
+organism <- "Homo sapiens"
+gene_filter <- "feature_id %in% c('ENSG00000107317', 'ENSG00000106034')"
+cell_filter <-  "cell_type == 'sympathetic neuron'"
+cell_columns <- c("assay", "cell_type", "tissue", "tissue_general", "suspension_type", "disease")
+
+seurat_obj <- get_seurat(
+   census = census,
+   organism = organism,
+   var_value_filter = gene_filter,
+   obs_value_filter = cell_filter,
+   obs_column_names = cell_columns
+)
+```
 
-## Example
+And the following retrieves the same data as a `SingleCellExperiment` object.
 
-This is a basic example which shows you how to solve a common problem:
+```r
+library("SingleCellExperiment")
 
-``` r
-library(cellxgene.census)
-## basic example code
+sce_obj <- get_single_cell_experiment(
+   census = census,
+   organism = organism,
+   var_value_filter = gene_filter,
+   obs_value_filter = cell_filter,
+   obs_column_names = cell_columns
+)
 ```
 
 ## For More Help
 
-For more help, please file a issue on the repo, or contact us at <soma@chanzuckerberg.com>
+For more help, please go visit the [main Census site](https://chanzuckerberg.github.io/cellxgene-census/). 
 
-If you believe you have found a security issue, we would appreciate notification. Please send email to <security@chanzuckerberg.com>.
+If you believe you have found a security issue, we would appreciate notification. Please send an email to <security@chanzuckerberg.com>.

api/r/cellxgene.census/docs/pkgdown.yml

@@ -8,5 +8,5 @@ articles:
   comp_bio_census_info: comp_bio_census_info.html
   comp_bio_data_integration: comp_bio_data_integration.html
   comp_bio_summarize_axis_query: comp_bio_summarize_axis_query.html
-last_built: 2023-08-02T19:37Z
+last_built: 2023-08-03T18:54Z
 

docs/cellxgene_census_docsite_installation.md

@@ -29,11 +29,21 @@ If installing in a Databricks notebook environment, use `%pip install`. Do not u
 
 ## R
 
-The R package will be soon deposited into R-Universe. In the meantime you can directly install from github using the [devtools](https://devtools.r-lib.org/) R package.
-
-From an R session:
+From an R session, first install `tiledb` from R-Universe, the latest release in CRAN is not yet available.
 
 ```r
-install.packages("devtools")
-devtools::install_github("chanzuckerberg/cellxgene-census/api/r/cellxgene.census")
+install.packages(
+  "tiledb",
+  version = "0.20.2", 
+  repos=c('https://tiledb-inc.r-universe.dev','https://cloud.r-project.org') 
+)
 ```
+
+Then install `cellxgene.census` from R-Universe.
+
+```r
+install.packages(
+  "cellxgene.census",
+  repos=c('https://tiledb-inc.r-universe.dev','https://cloud.r-project.org') 
+)
+```