inst/helpfiles/tabPanel_tSNE.md

In tnaake/MatrixQCvis: Shiny-based interactive data-quality exploration for omics data

t-distributed stochastic neighbor embedding (tSNE)

The panel depicts a plot of tSNE. The parameters Perplexity, Number of iterations, Number of retained dimensions in initial PCA, and Output dimensionality required for the tSNE algorithm can be set with the sliders. For the parameter Number of retained dimensions in initial PCA the panel Principal components can be employed that shows on the left panel a Scree plot of the data set and permuted values and corresponding p-values from the permutation. For computational reasons, the data set will be restricted to the top 5000 varying features based on their standard variation (only if there are more than 5000 features in the data set, otherwise all features are taken).

The different dimensions of the transformed data can be displayed by changing the values in the drop-down menus for the x-axis and y-axis (either two or three dimensions according to the Output dimensionality).

tnaake/MatrixQCvis documentation built on June 20, 2024, 7:22 a.m.