anvi-display-pan
Table of Contents
Start an anvi'o server to display a pan-genome.
🔙 To the main page of anvi’o programs and artifacts.
Authors
Requires
Provides
Can provide
svg 
collection 
bin 
gene-cluster-inspection 
Usage
This program displays the contents of a pan-db in the anvi’o interactive interface, much like anvi-interactive.
Like you can see in the pangenomics tutorial, this opens a window of the interactive interface where each item is a gene cluster and each layer represents one of your genomes.
A general run
You can run it with only two parameters:
anvi-display-pan -p pan-db \ -g genomes-storage-db
There are several default layer orders to choose from, including organizing based on gene cluster presence/absense or gene cluster frequency. These will both group your core gene clusters and singletons separately.
Beyond that, there are many different settings you can change in the side panel of the interface and you can import various additional data (primarily with the program anvi-import-misc-data). Once you’re happy with the data displayed in the interface (and the prettiness of that data), you can save those preferences in a state.
Item data groups
The inner layers of the pan display (gene cluster statistics, homogeneity indices, AAI values, etc.) are organized into data groups. When anvi-pan-genome generates a pan database, it stores related data in named groups such as gene_cluster_stats, SCG, homogeneity, and AAI. Any data you import with anvi-import-misc-data goes into the default group (or a group of your choosing via the -D flag).
In the Main tab of the interactive interface, you will find Item Data Groups checkboxes that let you toggle entire groups of layers on or off. This makes it easy to focus on specific aspects of your pangenome without manually hiding individual layers. Related layers within each group are kept together and visually separated from other groups by a small margin.
I want MORE data displayed
There are several other data types you can additionally choose to display in this program. Namely, you can add:
- a title (very fancy I know) using
--title - a NEWICK formatted tree (or import it as a misc-data-items-order-txt with anvi-import-items-order or as a misc-data-layer-orders with anvi-import-misc-data).
- view data in a tab-delimited file
- an additional view (provide this in a tab-delimited matrix where each column corresponds to a sample and each row corresponds to a gene cluster)
- an additional layer in the form of a misc-data-layers-txt (or import it into your pan-db with anvi-import-misc-data
How to minimize mouse clicks
Wondering how to autoload specific aspects of the interface? You’re in the right place.
You have the option to specify quite a few aspects of the interface through the parameters to save you those sweet mouse clicks.
- You can specify which view to start the interface with. Check which views are available with
--list-views. - You can load a specific state (either a previous state or a state that you’ve imported with anvi-import-state). Check which states are available with the flag
--list-states. - You can also load a specific collection with
--collection-autoload. To check which collections are availible, use--list-collections.
Other parameters
You can also skip processes like intializing functions or automatically ordering your items to save time, as well as configure the server to your heart’s content.
Edit this file to update this information.
Command line interface
The following is the list of parameters and their descriptions in the latest version of anvi-display-pan.
The code that generates this web page ensures that this information is the latest available in 9-dev (eunice). Which means, in some cases the information in this section (generated automatically) might be more comprehensive or up-to-date compared to the descriptions above (written by humans).
Command line usage
Parameters and their descriptions
-p, --pan-dbPAN_DB- Anvi'o pan database
-g, --genomes-storageGENOMES_STORAGE- Anvi'o genomes storage file
-d, --view-dataVIEW_DATA- A TAB-delimited file for view data
-t, --treeNEWICK- NEWICK formatted tree structure
-V, --additional-viewADDITIONAL_VIEW- A TAB-delimited file for an additional view to be used in the interface. This file should contain all split names, and values for each of them in all samples. Each column in this file must correspond to a sample name. Content of this file will be called 'user_view', which will be available as a new item in the 'views' combo box in the interface
-A, --additional-layersADDITIONAL_LAYERS- A TAB-delimited file for additional layers for splits. The first column of this file must be split names, and the remaining columns should be unique attributes. The file does not need to contain all split names, or values for each split in every column. Anvi'o will try to deal with missing data nicely. Each column in this file will be visualized as a new layer in the tree.
--skip-init-functions- When declared, function calls for genes will not be initialized (therefore will be missing from all relevant interfaces or output files). The use of this flag may reduce the memory fingerprint and processing time for large datasets.
--dry-run- Don't do anything real. Test everything, and stop right before wherever the developer said 'well, this is enough testing', and decided to print out results.
--skip-auto-ordering- When declared, the attempt to include automatically generated orders of items based on additional data is skipped. In case those buggers cause issues with your data, and you still want to see your stuff and deal with the other issue maybe later.
--skip-news- Don't try to read news content from upstream.
-I, --ip-addressIP_ADDR- IP address for the HTTP server. The default ip address (localhost) should work just fine for most. Default:
localhost -P, --port-numberINT- Port number to use for anvi'o services. If nothing is declared, anvi'o will try to find a suitable port number, starting from the default port number, 8080.
--browser-pathPATH- By default, anvi'o will use your default browser to launch the interactive interface. If you would like to use something else than your system default, you can provide a full path for an alternative browser using this parameter, and hope for the best. For instance we are using this parameter to call Google's experimental browser, Canary, which performs better with demanding visualizations.
--read-only- When the interactive interface is started with this flag, all 'database write' operations will be disabled.
--server-only- The default behavior is to start the local server, and fire up a browser that connects to the server. If you have other plans, and want to start the server without calling the browser, this is the flag you need.
--password-protected- If this flag is set, command line tool will ask you to enter a password and interactive interface will be only accessible after entering same password. This option is recommended for shared machines like clusters or shared networks where computers are not isolated.
--user-server-shutdown- Allow users to shutdown an anvi'server via web interface.
Additional Resources
Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.