Update README.md

README.md

@@ -2,23 +2,25 @@
 
 R Shiny app for comparison of annotations such as (i) cell type assignments (e.g., from different mapping/clustering algorithms), (ii) donor metadata (e.g., donor, sex, age), and (iii) cell metadata (e.g., anatomic location, QC metrics).  This tool is now **[hosted on shinyapps.io](https://sea-ad.shinyapps.io/ACEapp/)**.
 
-![image](https://github.com/AllenInstitute/ACE/assets/25486679/9bc32bb6-8245-4c5e-8ea0-b26be27fcab0)
-![image](https://github.com/AllenInstitute/ACE/assets/25486679/aef25d6d-f842-42d9-8b72-a65604b875b0)
+![main_ACE_app_page_top](https://github.com/user-attachments/assets/51375516-0203-45d7-a207-6f91a08140df)
 
+Additionally, this tool can compare results across more than two taxonomies at once. The three primary use cases are (1) annotating a novel taxonomy with information from multiple existing taxonomies (e.g., after running [MapMyCells](https://portal.brain-map.org/atlases-and-data/bkp/mapmycells)), (2) comparing cell type names between different taxonomies on [Allen Brain Map](https://portal.brain-map.org/cell-types), and (2) comparison of data from multiple studies of Alzheimer's disease (like in the example below).
 
-Additionally, this tool can compare results across more than two taxonomies as once. The two primary use cases are (1) annotating a novel taxonomy with information from multiple existing taxonomies and (2) comparison of data from multiple studies of Alzheimer's disease (like in the example below).
+## How to use 
 
-![multi_comparison](https://github.com/AllenInstitute/annotation_comparison/assets/25486679/c55dac6e-99f6-4fd6-9203-70e136cef9a7)
+### Visit the website
 
-## How to use 
+**We recommend using the version of this tool [hosted on shinyapps.io](https://sea-ad.shinyapps.io/ACEapp/)**. 
 
-Either visit the tool **[hosted on shinyapps.io](https://sea-ad.shinyapps.io/ACEapp/)** or follow the instructions below to run locally in R Studio.  Currently, you need to run it locally to point to external files stored locally, but for most use cases, the hosted version is recommended.
+### Run locally
 
-### Setup RStudio
+For power users, this tool can also be run locally in R Studio by following the steps below.
+
+#### Setup RStudio
 (You only need do this step once).
 1. Install R
 2. Install RStudio
-3. Install the following packages in R Studio:
+3. Install the following packages in R Studio**:
 ```
 options(install.packages.compile.from.source = "always")
 packages <- setdiff(c("remotes","dplyr","data.table","DT","feather","ggplot2","ggbeeswarm","shiny","UpSetR","anndata"), installed.packages()[,"Package"])
@@ -28,13 +30,33 @@ remotes::install_github("bokeh/rbokeh")
 ```
 4. Download the files from this repo (you may want to repeat this step occasionally to check for updates!) 
 
-### Run the app
+**If there are issues with setup in step #3, note that the complete R environment is saved [in the renv folder](https://github.com/AllenInstitute/ACE/tree/main/renv).
+
+#### Run the app
 1. In RStudio, open the file `ui.R` and click the "Run App" button in the upper right corner of the screen
-2. Enter the location of your annotation file in the "Location of annotation information" box (it *should* be pointing to some example data by default)
-3. Explore!
+2. Explore!
+
+The only difference between local and web versions is that the local version can point to locations on your local computer (which in most cases is unnecessary as these can be uploaded on the web version).
 
 ## Reporting issues or suggestions
 
 Please share any comments, suggestions, bugs, or any other thoughts using the button in the app, or by [submitting an issue](https://github.com/AllenInstitute/ACE/issues).
 ![image](https://github.com/AllenInstitute/ACE/assets/25486679/a0e2ee8d-5315-400d-a723-b9bb9719c4bd)
 
+## License
+
+The license for this package is available on Github at: https://github.com/AllenInstitute/ACE/blob/master/LICENSE
+
+## Level of Support
+
+We are actively updating this tool. **Community involvement is encouraged through both issues and pull requests.**
+
+## Example visualizations and Acknowledgements
+
+### Confusion matrices
+
+![main_ACE_app_page_bottom](https://github.com/user-attachments/assets/4fd8eb94-5700-4c79-8729-e2bf6cfb34f3)
+
+### Comparing matched cell types across studies of AD
+
+![multi_study_comparison_ACE_panel](https://github.com/user-attachments/assets/31c68130-3159-4d00-88d1-dd0a253bc5a2)