Import data after clustering from R

[Tommy Tang]

USE CASE: WHAT DO YOU WANT TO DO?

Import clustering results generated from R to apply to an existing matrix.

STEPS TO REPRODUCE AN ISSUE (OR TRIGGER A NEW FEATURE)

1. File->Import clustered data
2. Choose, rows/cols & validate associations

CURRENT BEHAVIOR

No ability to apply clustered results from 3rd party clustering methods to an existing matrix

EXPECTED BEHAVIOR

Ability to apply cluster results to existing matrix data.

DEVELOPERS ONLY SECTION

SUGGESTED CHANGE (Pseudocode optional)

Import wizard that matches row/column labels to the cluster leaf labels

FILES AFFECTED (where the changes will be implemented) - developers only

new classes

LEVEL OF EFFORT - developers only

major

COMMENTS

Original request:

feature request: import data after clustering from R. rotate dendrogram

Hi,

Thanks very much for this very useful tool.
I usually do clustering using R, how can I import the clustered data matrix into treeviewer and maintain the dendrograms?

for clustering, can one click on the nodes and rotate the denderogram? flipping the dendrogram does not change  the clustering, but sometimes may look better.

Thanks very much!

Ming

See issue #523 for tree rotation.

[Robert Leach]

I had brought up the ability to rotate subtrees before, but I don't think it became an issue, though it's mentioned in the last comment in issue #33.

I will break up this feature request into the 2 separate suggestions (import dendrograms output by R & rotate tree nodes).

[Robert Leach]

Applied issue form & split into 2 separate issues.

[Tommy Tang]

Thanks!

I read issue #33, it will be really nice to have more flexibility to manipulate the dendrogram, like dendextend does https://cran.r-project.org/web/packages/dendextend/vignettes/introduction.html, specifically change the order of the rows and columns.

I am not sure the what is the vision of the development of this tool. one thing can be useful is to be able to compare clusters for two or more heatmaps. the same feature(rows) can be connected with ribbon bands.something like http://caleydo.org/tools/stratomex/, I never learned to use stratomex. Ideally, one tool should be useful but also easy to use. I like the simplicity of treeview in this perspective.

[Robert Leach]

Yes, we have a series of matrix editing issues slated, though at the moment, they are not slated for the next major release. We need to come up with a whole editing paradigm first that will enable editing.

[Robert Leach]

If you see issues you like, please vote for them using the vote link at the top-right of the issue details.

[Tommy Tang]

sure, will do.

Thanks for the user support!