Merge pull request #29 from AlexsLemonade/jashapiro/readme-update

Add more content to readme and update pkgdown

Author: jashapiro

DESCRIPTION

@@ -11,9 +11,22 @@ Authors@R: c(
     )
 Description: An R package to interact with the Single-Cell Pediatric Cancer Atlas Portal API.
 License: BSD_3_clause + file LICENSE
+URL: https://alexslemonade.github.io/ScPCAr, https://github.com/AlexsLemonade/ScPCAr
+BugReports: https://github.com/AlexsLemonade/ScPCAr/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
+Imports:
+    curl,
+    dplyr,
+    glue,
+    httr2 (>= 1.2.0),
+    purrr,
+    readr,
+    stringr,
+    tibble,
+    tidyr,
+    utils
 Suggests:
     devtools,
     ggplot2,
@@ -27,15 +40,3 @@ Suggests:
     withr
 Config/testthat/edition: 3
 VignetteBuilder: knitr
-Imports:
-    curl,
-    dplyr,
-    glue,
-    httr2 (>= 1.2.0),
-    purrr,
-    readr,
-    stringr,
-    tibble,
-    tidyr,
-    utils
-URL: https://alexslemonade.github.io/ScPCAr/

README.md

@@ -4,4 +4,41 @@ An R package for interacting with the [Single-cell Pediatric Cancer Atlas (ScPCA
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/AlexsLemonade/ScPCAr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/AlexsLemonade/ScPCAr/actions/workflows/R-CMD-check.yaml)
- <!-- badges: end -->
+<!-- badges: end -->
+
+## Installation
+
+The `ScPCAr` package can be installed from the GitHub repository using the `remotes` package:
+
+```r
+remotes::install_github("AlexsLemonade/ScPCAr")
+```
+
+## Usage
+
+The package provides functions to get metadata and download data from the ScPCA Portal from within R. 
+The code chunk below shows an example of how to authenticate and download a single sample from the portal.
+
+```r
+library(ScPCAr)
+
+# First, look at the terms of use
+view_terms()
+
+# Get an authentication token for use with the ScPCA Portal
+auth_token <- get_auth(email = "your.email@example.com", agree = TRUE)
+
+# Get the sample metadata for a project
+sample_metadata <- get_sample_metadata(project_id = "SCPCP000001")
+
+# Download a data for a sample
+# this function returns a vector of the downloaded file paths
+file_paths <- download_sample(
+  sample_id = "SCPCS000001",
+  auth_token = auth_token,
+  destination = "scpca_data",
+  format = "sce"
+)
+```
+
+For detailed usage instructions, please refer to the [package documentation](https://alexslemonade.github.io/ScPCAr/).

_pkgdown.yml

@@ -3,6 +3,15 @@ template:
   bootstrap: 5
   light-switch: true
 
+home:
+  links:
+    - text: The ScPCA Portal
+      href: https://scpca.alexslemonade.org/
+    - text: Alex's Lemonade Stand Foundation
+      href: https://alexslemonade.org/
+    - text: The Childhood Cancer Data Lab
+      href: https://www.ccdatalab.org
+
 reference:
   - title: Metadata
     contents: