caleydo / stratomex_js

StratomeX for the visual exploration of genomic stratification of diseases @JKU-ICG

stratomex_js

StratomeX.js is a port for Phovea using the Caleydo CLUE framework for provenance tracking and story telling.

Further resources:

• Vistories.org
• CLUE Homepage
• Examples using CLUE: StratomeX and Gapminder

A demonstration is available in the caleydoapp.org.

Installation

git clone https://github.com/caleydo/stratomex_js.git
cd stratomex_js
npm install

Testing

npm test

Building

npm run build

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This repository is part of Phovea, a platform for developing web-based visualization applications. For tutorials, API docs, and more information about the build and deployment process, see the documentation page.

stratomex_js's Issues

band are not shown except the last one

• Release number or git hash: b7a47f5
• Web browser version and OS: chrome, win 10
• Environment (local or deployed): local

Steps to reproduce

1. select 3 columns

Observed behavior

see just the last bands between column 2 and 3 but not between 1 and 2

Expected behavior

no bug ;)

Get Travis passing again

Follow up from #14 (comment): Travis used to pass, and it no longer does, but I am not sure what changed: unpinned dependencies, perhaps?

Decrease width of categorical columns

Width should be about the same as in the original StratomeX

create kaplan meier vis

Issues with detail heatmaps

I'm having troubles with the detail views. Opened a details view:

Closed it:

change locators to just use the whole groups and not individual items

important when changing the view from heatmap to e.g. histogram for a cluster

Merge Michael’s StratomeX extensions into master branch

heatmap scaling and/or rendering issue

• Release number or git hash: current deployment on stratomex.caleydoapp.org
• Web browser version and OS: lasted Mac OS X and latest Chrome
• Environment (local or deployed): deployed

Steps to reproduce

1. Go to https://stratomex.caleydoapp.org/#clue_graph=clue_stratomex0&clue=P&clue_slide=96&clue_state=93

Observed behavior

• the heatmaps look like they are not scaled or not rendered correctly (too much red)

Expected behavior

• correctly scaled and correctly rendered heatmaps

Fix layout of detail mode for columns

Remove lazy lineup columns on error

Server-side similarity calculation adds lazy columns which should be removed if the task fails:
https://github.com/Caleydo/stratomex_js/blob/keckelt/jaccardGroupCmp/src/index.ts#L91

Selection state of a group is not reset

• Release number or git hash: latest | 995446c
• Web browser version and OS: Chrome 58.0.3029.81 (64-bit) @ Fedora 23 Workstation
• Environment (local or deployed): local

Steps to reproduce

1. Add 1 or more columns with 2 or more groups
2. Select a group by clicking on title
3. Change selection by clicking on another group's title of the same column --> Selection changes as expected
4. Select group of Step 2 again. --> No group is selected (the group of step 2 deselected)
5. Select group of step 3 again --> No group is selected (the group of step 3 is now deselected)

Observed behavior

The phovea-select-selected attribute is not removed when another group gets selected, thus the d3.select method is called with false parameters.

Expected behavior

When clicking on a group, it should become selected.

how to coordinate multiple cluster groups

e.g. use the same max value for all histograms in a column
coordinate the kaplan meier plot axis scales

scaling in detail view and selection within the heatmap

columns should not contain data package in label

• Release number or git hash: latest
• Web browser version and OS: chrome
• Environment (local or deployed): local

Create Detail View

band rendering issue when adding categorical columns

Tested with currently deployed version that is available at stratomex.caleydoapp.org.

Also allow numerical axes to be added to stratomex

Upgrade tsconfig library

Creating a new workspace with the stratomex_product, it can not compile due to phovea_core using Array.prototype.includes()

Error message:

ERROR in [at-loader] ../phovea_clue/src/internal.ts:98:29 
    TS2339: Property 'includes' does not exist on type 'string[]'.

ERROR in [at-loader] ../phovea_clue/src/internal.ts:98:99 
    TS2339: Property 'includes' does not exist on type 'string[]'.

Changing the es2015 lib to es2016 did fix the errors for me locally: https://github.com/Caleydo/stratomex_js/blob/master/tsconfig.json#L12

Probably missing quote symbol

• Release number or git hash: latest

Missing Quote " After column name?

Column.ts Line 175:
return action(meta('set option "' + name + +'" of "' + column.name + ' to "' + value + '"', cat.visual), 'setStratomeXColumnOption', setOption, [column], {
--> set option "NAME" of "COLUMN.NAME to "VALUE"
instead of:
--> set option "NAME" of "COLUMN.NAME" to "VALUE"

add dependent data doesn't work

'+' button doesn't appear

Get datset is blocked after token timeout

• Release number or git hash: latest
• Web browser version and OS: chrome 60
• Environment (local or deployed): local

Steps to reproduce

1. Open StratomeX
2. Add a dataset from lineup
3. Wait 10 minutes
4. Add another dataset -> nothing happens
5. Add a third dataset -> this and dataset of step 4 are added

Observed behavior

• At Step 4, the only log message is:
  18:52:54 INFO tourguide_data_calumma.calumma: releasing token f758747fa3284efaa2a4d5fa4dce174d

• Step 4 stops in tokenpool.py's getter after the old token is released.

Height scaling bug of stratomex in combination with data browser

ribbons broken when restoring shared vistory (also: browser differences)

Reproduce
http://demo.caleydo.org/stratomex.js/#clue_graph=workspaceForStratomexJsEa34Y&clue=A&clue_slide=96&clue_state=93

Observed
Chrome:

Safari:

Expected
View as in Chrome.

All copy number genes show the same stratification