diff --git a/conekt/static/js/planet_svg.js b/conekt/static/js/planet_svg.js index 9eceb98..ab05ae5 100644 --- a/conekt/static/js/planet_svg.js +++ b/conekt/static/js/planet_svg.js @@ -112,7 +112,7 @@ function writeSVG(data) { } text = node.data('name'); - if (node.data('gene_name') !== '') { text = node.data('gene_name'); } + if (node.data('best_name') !== '') { text = node.data('best_name'); } group.text({y:6, fill:"none", stroke:'#888888'}).content(text) .attr('text-anchor', 'middle') diff --git a/docs/building/003_expression_profiles.md b/docs/building/003_expression_profiles.md index a3b69eb..b544081 100644 --- a/docs/building/003_expression_profiles.md +++ b/docs/building/003_expression_profiles.md @@ -33,7 +33,7 @@ SRR314816 ... ``` -For profile plots on the website most likely a custum order of conditions +For profile plots on the website most likely a custom order of conditions is preferred. (We usually order tissues from bottom to top) A file to specify this needs to be provided, conditions need to be stated in the orther they should appear in the plot. @@ -57,4 +57,13 @@ If all files are selected click 'Add Expression Profiles' to upload the data and add everything to the database. -![Add expression profiles](../images/add_expression_profiles.png) \ No newline at end of file +![Add expression profiles](../images/add_expression_profiles.png) + +## Adding summarized profiles + +In case the complete profile is to detailed and more general profiles need to be included +(useful for specificity searches), there is the option to combine multiple condition in one. + +## Calculating expression specificity + +*UNDER CONSTRUCTION* \ No newline at end of file diff --git a/docs/building_conekt.md b/docs/building_conekt.md index f5b4b1b..f93f419 100644 --- a/docs/building_conekt.md +++ b/docs/building_conekt.md @@ -4,7 +4,14 @@ Make sure *LOGIN_ENABLED=True* in *config.py* and the database was build with and admin account (check [here](install_linux.md) for instructions -how to add an admin account). Next, go to the website, log in and (once logged +how to add an admin account). + +Make sure your server **doesn't time out requests**, some operations can take several +minutes. If your server is live already running build steps can result in issues for +active users. To avoid this consider running and extra CoNekT instance +on the server using the built in web-server and connecting to it using an SSH tunnel. + +To start building, go to the website, log in and (once logged in) click on the username (admin) in the top right corner. Select 'Admin Panel' from the drop-down menu. @@ -23,7 +30,7 @@ Step-by-step instructions * [Adding GO term and InterPro domain definitions](./building/001_GO_InterPro_domains.md) * [Adding a new species and functional data](./building/002_species_functional_data.md) - * [Adding expression profiles](./building/003_expression_profiles.md) + * [Adding expression profiles and specificity](./building/003_expression_profiles.md) * [Adding co-expession networks and clusters](./building/004_coexpression_network_cluster.md) * [Adding comparative genomics data](./building/005_comparative_genomics.md) * [Precomputing counts and more](./building/006_precomputing_counts_etc.md)