k3rn1n4tor / stratomex_js

StratomeX app in Caleydo Web with rudimentary Provenance support

StratomeX - Clustering [Fork]

This is a fork of the original StratomeX repository to integrate dynamic, server-side clustering on genomic data and analyze the confidence or ambiguity of cluster assignments. It is implemented as Caleydo web plugin: https://github.com/Caleydo/caleydo_web

Demo-Version of the tool: http://ec2-52-58-105-31.eu-central-1.compute.amazonaws.com/

Features:

• Supports application of clustering algorithms (k-means, hierarchical, affinity propagation, fuzzy) to genomic data.
• Creates views showing the distances/correlation/probability of each record in one cluster to the cluster centroid and the distances/correlation/probability of each patient to all other cluster.
• Provides splitting of one cluster into three different subsets (well-fitting, uncertain, bad-fitting) to further analyze how well the records fit into one cluster.
• Supports refinement of clusters/groups (shifting to better fits, merging, exclusion)
• Support dynamical increase/reduction of the number of clusters in hierarchical cluster results.

Installation:

• Checkout caleydo_web_container: https://github.com/Caleydo/caleydo_web_container
• Checkout calyedo_clustering: https://github.com/K3rn1n4tor/caleydo_clustering
• Update all other repos to the latest version (at least from March 21st).
• Make sure you have the caleydo_data_hdf (required for TCGA data) and caleydo_vis_lineup plugin.

Future Work:

• See Issues section for further information.

stratomex_js's Issues

Add new feature to cluster data on the fly

Axis for Kaplan-Meier-Plots

Re-cluster stratification

Based on user-specified divisions and distance of each division to the other divisions

Support for all Browsers

Make sure that layout is consistent in every browser!

Rescaling of Window / Viewport should not affect Slider Height

Custom Popup for clustering data

Consider to implement box containing all cluster algorithm for either one cluster algo group or all kind of groups

Hierarchical Clustering And Interactive Cutting Tool

Implement button to show Column where dendrogram is shown in a separate view alongside the original matrix. Provide a slider to cut dendrogram and show result in a new column.

Change External View Vis

Separate external views from internal distance view, shift them and provide views for all clusters within the new view (one should be empty for each cluster)
Same for matrix view except the vertical bar chart showing the internal distances remains visible all the time.

Distance computation yields NaN values for some metrics

Try to detect error and fix it! Or eliminate all NaNs.

Enable Clustering with Supported Distance Metrics

Change color coding for all the views

Kaplan-Meier Plots

Check if KM Plots can be displayed alongside the cluster columns to display the changes of these plots.

Preserve connections of split-columns to unchanged groups

Allow user to merge more than one division at a time

Bug: Regrouping of Fuzzy Column not working

Somehow some subsets of the matrix cannot be accessed (index error). Try to figure out what's wrong here.

Excluding / Merging of Groups within Cluster

Excluding is possible now, and can be reverted.

Add statistics window to cluster column as separate view

Merging two clusters

Show difference matrix alongside a column using the same stratification

What's a good measurement for the distance between two patients?

Perhaps hide sliders when distance view is not selected?

Use TCGA Data

Enhance affinity performance

Add new button and column for clustering in LineUp

Maybe look for alternative cluster number selection besides the normal prompt dialog

Add annotations / tooltips to every button

Helps to control application

Colorize patient lines or ribbons to make clear which patients correspond to which cluster group

Merge with latest Caleydo repositories

Fully Support Provenance Graph

Find a way to upload dendrogram and partition matrix to support the provenance graph!

Support all stats views for one column and stats views for columns displaying the same data

Show cluster distances of each patient in one cluster to the centroids of all other clusters

Add column for certain/uncertain/outlier groups

Try to create new column that contains new multigrid of the subdata of one cluster --> create 3 new clusters based on the histogram slider that divides subdata into three groups.

Run clustering algorithms on subsets?

What about allowing the user to run clustering algorithms on subsets / clusters itself?
Compare results with manual refinement?
Allow back-merging of the stratification?

Convert LineUp to Typescript

Show Distances in Form of Heatmap

To support more than 10 clusters. Enable switching between bar charts and matrix view.

Create new class cluster column and integrate clusterDivider into Multiform

Should support provenance graph, as well!

Support Interactive Exploration of Fuzzy Clustering

Combine fuzzy clustering with other fuzzy / discrete clustering algorithm to create a new fuzzy clustering and to obtain a discrete stratification from the result.

Enhance Slider Drag-Movement Behavior

Does Caleydo change name?

Hi!

I've trying to run locally, but I didnt get success.
Can you help?

Do you have this code in another local?

Thanks!

Implement Histogram Slider as Multiform Vis

Integrate Histogram Slider as view at the top of the column