1. Select data matrix
Choose the data matrix as your input file. This file should be csv format with ',' seperation.
See example data matrix.
2. Run on example dataWe provide 6 example data matrices for you to run. You can choose one of them. If you upload input data, we will calculate the biclusters for the uploaded one, otherwise we will run the example data which you choose (default data matrix is preseident.csv).
3. Parameter setting
These parameters are related to the convex biclustering algorithm for computing the row and column hierarchical clusterings
4. Submit or cancel the uploaded files
Click submit to submit the job, or click Cancel to clear the uploaded files.
If you already have the output json file that was produced by our standalone convex biclustering program, you can upload the output .json file and visualize it on our website.
After a valid submission, you will be given a unique ID to track your job status. Wait for some time (typically a few seconds) and you will see the result page. If you want to bookmark, please save the link of this, which will give you the result once the job is done.
The result page includes the row and column clustering dendrogram, and the corresponding heatmap.
At the top of the figure, you can select different gammas and the heatmap will display the solution matrix with respect to the gamma you chose.In addition, you can also download the figure with png or csv format.
Here, rowJSON represent the tree for the row dendrogram. colJSON represent the tree for the column dendrogram. The D3.js will use the depth first search (DFS) algorithm to reorder the leaf nodes in the dendrogram. And the heatmap will also be rearranged according to the order of leaf nodes.