NBF_vis: Neighborhood-Based Featurization Visualization

In XTH1114/NBFvis: Visualization of Neighborhood-Based Features

Neighborhood-Based Featurization Visualization

Description

The function could apply UMAP to the featurization matrix of a special omics dataset.
This matrix could be a neighborhood matrix, which is the combination of the quantile
matrix and network matrix (from quantile_matrix and network_matrix, respectively)
Then, a shiny app will visualize the UMAP embeddings of the spatial omics data.

Usage

NBF_vis(matrix, origin_data, var_names)

Arguments

matrix	a statistics matrix. It should be rescaled. For example, it could be the rescaled quantiles network centralities matrix.
origin_data	a data frame. It is the origin dataset of cell expressions, like proteins and genes. Column index, Group, x_center and y_center should be included.
var_names	the names of columns about expressions like proteins or genes in the argument origin_data.

Value

an interactive shiny app for the UMAP embeddings.

XTH1114/NBFvis documentation built on Sept. 14, 2022, 1:13 p.m.