From 8dc4ec9c8f2ac9b2c3733103cb30ecfcc0aed80d Mon Sep 17 00:00:00 2001 From: Scooter Morris Date: Wed, 17 Mar 2021 20:34:18 -0700 Subject: [PATCH] Some simple command updates --- .../edu/ucsf/rbvi/scNetViz/internal/CyActivator.java | 10 +++++----- .../scNetViz/internal/sources/file/FileSource.java | 2 +- .../rbvi/scNetViz/internal/sources/hca/HCASource.java | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/src/main/java/edu/ucsf/rbvi/scNetViz/internal/CyActivator.java b/src/main/java/edu/ucsf/rbvi/scNetViz/internal/CyActivator.java index e0773fb..72ca886 100644 --- a/src/main/java/edu/ucsf/rbvi/scNetViz/internal/CyActivator.java +++ b/src/main/java/edu/ucsf/rbvi/scNetViz/internal/CyActivator.java @@ -154,7 +154,7 @@ public void start(BundleContext bc) { props.setProperty(IN_MENU_BAR, "TRUE"); props.setProperty(COMMAND_NAMESPACE, "scnetviz"); props.setProperty(COMMAND, "calculate tSNE"); - props.setProperty(COMMAND_DESCRIPTION, "Calculate the tSNE embedding"); + props.setProperty(COMMAND_DESCRIPTION, "Calculate the tSNE embedding (local)"); props.setProperty(COMMAND_LONG_DESCRIPTION, ""); props.setProperty(COMMAND_SUPPORTS_JSON, "true"); props.setProperty(COMMAND_EXAMPLE_JSON, "{}"); @@ -171,7 +171,7 @@ public void start(BundleContext bc) { props.setProperty(IN_MENU_BAR, "TRUE"); props.setProperty(COMMAND_NAMESPACE, "scnetviz"); props.setProperty(COMMAND, "calculate UMAP"); - props.setProperty(COMMAND_DESCRIPTION, "Calculate the UMAP embedding"); + props.setProperty(COMMAND_DESCRIPTION, "Calculate the UMAP embedding (remote)"); props.setProperty(COMMAND_LONG_DESCRIPTION, ""); props.setProperty(COMMAND_SUPPORTS_JSON, "true"); props.setProperty(COMMAND_EXAMPLE_JSON, "{}"); @@ -235,7 +235,7 @@ public void start(BundleContext bc) { Properties props = new Properties(); props.setProperty(COMMAND_NAMESPACE, "scnetviz"); props.setProperty(COMMAND, "show cell plot"); - props.setProperty(COMMAND_DESCRIPTION, "Display the cell plot for a single experiment"); + props.setProperty(COMMAND_DESCRIPTION, "Display the current cell plot (UMAP, t-SNE) for a single experiment"); props.setProperty(COMMAND_LONG_DESCRIPTION, ""); props.setProperty(COMMAND_SUPPORTS_JSON, "false"); scNVManager.registerService(show, TaskFactory.class, props); @@ -299,7 +299,7 @@ public void start(BundleContext bc) { Properties props = new Properties(); props.setProperty(COMMAND_NAMESPACE, "scnetviz"); props.setProperty(COMMAND, "create all"); - props.setProperty(COMMAND_DESCRIPTION, "Create networks"); + props.setProperty(COMMAND_DESCRIPTION, "Calculate differential expression and create networks"); props.setProperty(COMMAND_LONG_DESCRIPTION, "Use default cluster to calculate differential expression and create networks."); props.setProperty(COMMAND_SUPPORTS_JSON, "true"); props.setProperty(COMMAND_EXAMPLE_JSON, "{}"); @@ -311,7 +311,7 @@ public void start(BundleContext bc) { Properties props = new Properties(); props.setProperty(COMMAND_NAMESPACE, "scnetviz"); props.setProperty(COMMAND, "calculate diffexp"); - props.setProperty(COMMAND_DESCRIPTION, "Calculate the table of differential expressions"); + props.setProperty(COMMAND_DESCRIPTION, "Calculate the table of differential gene expression"); props.setProperty(COMMAND_LONG_DESCRIPTION, ""); props.setProperty(COMMAND_SUPPORTS_JSON, "true"); props.setProperty(COMMAND_EXAMPLE_JSON, "{}"); diff --git a/src/main/java/edu/ucsf/rbvi/scNetViz/internal/sources/file/FileSource.java b/src/main/java/edu/ucsf/rbvi/scNetViz/internal/sources/file/FileSource.java index 106b837..a80856a 100644 --- a/src/main/java/edu/ucsf/rbvi/scNetViz/internal/sources/file/FileSource.java +++ b/src/main/java/edu/ucsf/rbvi/scNetViz/internal/sources/file/FileSource.java @@ -71,7 +71,7 @@ public FileSource (ScNVManager manager) { props.setProperty(IN_MENU_BAR, "TRUE"); props.setProperty(MENU_GRAVITY, "30.0"); props.setProperty(COMMAND_NAMESPACE, "scnetviz"); - props.setProperty(COMMAND_DESCRIPTION, "Load an experiment from a file"); + props.setProperty(COMMAND_DESCRIPTION, "Load an experiment from a MatrixMarket file"); props.setProperty(COMMAND, "load experiment file"); scNVManager.registerService(new FileExperimentTaskFactory(manager, this), TaskFactory.class, props); } diff --git a/src/main/java/edu/ucsf/rbvi/scNetViz/internal/sources/hca/HCASource.java b/src/main/java/edu/ucsf/rbvi/scNetViz/internal/sources/hca/HCASource.java index b8bb238..843c085 100644 --- a/src/main/java/edu/ucsf/rbvi/scNetViz/internal/sources/hca/HCASource.java +++ b/src/main/java/edu/ucsf/rbvi/scNetViz/internal/sources/hca/HCASource.java @@ -86,7 +86,7 @@ public HCASource (ScNVManager manager) { // Register our commands { Properties props = new Properties(); - props.setProperty(COMMAND_DESCRIPTION, "List all Gene Expression Atlas (HCA) entries available"); + props.setProperty(COMMAND_DESCRIPTION, "List all Human Cell Atlas (HCA) entries available"); props.setProperty(COMMAND_NAMESPACE, "scnetviz"); props.setProperty(COMMAND, "list hca entries"); props.setProperty(COMMAND_SUPPORTS_JSON, "true");