Matrix upload

Upload a matrix in a csv or RDS file

Maximun file size = 30Mb (~ 600 x 5000 matrix)

Choose a .csv or .RDS File

Browse...

Click Demo

to load Corces-Buenrostro AML dataset

NMF params

Minimum factorization rank:

Maximum factorization rank:

Select factorization method:

Number of initializations:

Convergence threshold:

Annotation upload

Upload a table with annotation data in a csv or RDS file

The first column should match the column names in the input matrix

Choose a .csv or .RDS File

Browse...

Start NMF

Click 'Submit' button to start running NMF in the uploaded matrix and with selected parameters

ShinyButchR

ShinyButchR is an app to run Non-Negative Matrix Factorization (NMF) on a small input matrix using the Bratwurst package

You can explore the results in the NMF plots tab, or download the resulting H and W matrices in the save results tab.

ShinyButchR was developed by the Biomedical Genomics Group @ Health Data Science Unit at the BioQuant Center and Medical Faculty Heidelberg

Visit us here!

If you have any suggestion please create an issue in our GitHub repository hdsu-bioquant/ShinyButchR

Factorize

Factorized uploaded matrix

NMF plots

Displays the optimal factorization rank metrics

Displays a heatmap of the H matrix for each factorization rank

Displays a riverplot of all factorization ranks

Save results

saves all the results as RDS objects

H Matrix Heatmap

Column names

Cluster rows

Cluster columns

Show annotation

H Matrix UMAP

Recovery Plots

Optimal factorization rank

Based on the results of the factorization quality metrics, the optimal number of signatures (k)

Minize the Frobenius error, the coefficient of variation and the mean Amari distance

Maximize the sum and mean silhouette width and the cophenic coefficient.

NMF riverplot

Riverplot or Sankey diagram showing the similarity between signatures across factorization ranks

cutoff of displayed similarities:

Signature Specific Features Heatmap

Top % of associated features per signature:

Column names

Cluster rows

Cluster columns

Selected Signature Specific Features Heatmap

Download Signature Specific Features table

Select format

Download

Save NMF object

Save NMF object to use later in R

Download

This object is compatible with the latest version of ButchR

To install in R use:

remotes::install_github('wurst-theke/ButchR')

Save H and W matrices

Save the H matrix or the W matrix in csv or RDS format

Select Matrix

Select format

Download