Data visualization with t-SNE and UMAP
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Description
Recently, non-linear dimension-reduction and visualization algorithms, most notably t-Distributed Stochastic Neighbor Embedding (t-SNE) and uniform manifold approximation and projection (UMAP), have been widely applied to various research areas such as image processing, text mining, and genomics. This Add-in provides access to both t-SNE and UMAP R packages. It offers a user-friendly interface enabling data table navigation, data quality control, sparsity handling, intuitive parameterization, and interactive results interpretation.
Usage Example
Here is a screenshot of the interface with MNIST data loaded. Under Model Specifications, I selected the label column as Label and all the pixels as predictors. I chose both t-SNE and UMAP as the algorithms.
Another screenshot of the results of both t-SNE (top) and UMAP (bottom).
This add-in also supports some basic quality control options, including missing value checking, distribution, and sparsity calculation. You can find these options under Quality Control Options on the interface.
Updates: JMP R interface on Mac has versioning issues. Please downgrade your R to version <=3.3.3, and use t-sne only if you are a Mac user.
Changelog:
v.2 <9/22/2020> Added tsne and umap results to the original table and reorganized output for better exploration experience.
v.1.2 <3/14/2019> Fixed an issue in Rtsne package where a large number of columns causing stack overflow problem.
v.1.1 <3/8/2019> Fixed a bug that could potentially produce “issues found in R, memory exhausted?” error message. Added a submenu for the MNIST example dataset.
v.1.0 <2/26/2019> Initial version.
Hello,
I am getting this error. I've re-installed R 4.03 and UMAP in the cran package. The connection is there, but something isn't connecting.
{"UMAP"}
{3, 15, 200, 0.1}
"Got algr!"
"Got parameters!"
"Start inDataPrep"
{"2,3,7,8-TCDD", "1,2,3,7,8-PeCDD", "1,2,3,4,7,8-HxCDD", "1,2,3,6,7,8-HxCDD", "1,2,3,7,8,9-HxCDD", "2,3,7,8-TCDF", "1,2,3,7,8-PeCDF", "2,3,4,7,8-PeCDF", "1,2,3,4,7,8-HxCDF", "1,2,3,6,7,8-HxCDF"}
"Finish Sparsity"
"Sparsity is: "
0.280112044817927
"Label is: "
{}
"Dim of inData2R is: "
119
15
"Finished data preparation."
"Start backend!"
"Label is: "
{}
"Within talk2R function."
"label is:"
{}
"UMAP is selected!"
TKIntRJMP.R version 14.0
The final R statement is incomplete.
Send data for "data4R" failed
Good evening, dear colleagues!
I have installed R 3.6.3 and RStudio on my Windows 10 (64 bit). Installed both packages successfully and the example file for the add-in worked out well properly visualizing the data. However, as long as I launched my file (32 rows, 7 columns of the predictors, 1 column as "label"), the process resulted in an alert below.
Could you please, explain, what was wrong. All the columns were numerical-continuous like in the example, MNIST.jmp. The only difference was that the numbers in 7 variables were non-integer: like 0.234234 ou 0.472343.
I will highly appreciate your advice.
Michael
