Inferred Ancestry Dashboard

Select one or more rows in the Table tab.

Population-specific accuracy confidence intervals

Admixture proportions by molecular profile

Select populations in priority order, or drag tags to reorder. Bars sort by highest share of the first population, then ties by the second, and so on.

Introduction

This application is designed to interactively visualize genetic ancestry inferred from human molecular data other than whole-genome or whole-exome sequences of cancer-free DNA. Some examples of data it can handle includes targeted gene panels, RNA, whole genomes and whole exomes that can all include cancer-derived nucleic acids.
Source code and additional information for this application are available via the Inferred Ancestry Dashboard GitHub repository

Application usage

The application has three main features for analyzing inferred ancestry from cancer-derived molecular data: a map, a data table, and a set of plots given the selected data. For each sample selected in the table, a plot of the population-specific ancestry accuracies and their confidence intervals for the full set of populations that the inference method is trained on as well as for the inferred ancestry of the selected biosample. These plots are generated in the Plots tab and the user can scroll through the plots for each selected sample using the buttons at the bottom of the page.

Table Sample Selection

Table Sample Selection

Confidence Interval Plots

Confidence Interval Plots

The Plots tab also contains a subtab for viewing the Admixture plot. Users can choose to view the admixture proportions for all the samples in the table or only samples that were selected in the table. The stacked bar plot displays the samples on the x-axis and the proportion of the admixture of each population in the sample on the y-axis. The stacked bar plot is color-coded by population. Users have the option to sort samples by population proportion amount. Users can add to the input selection the order of populations to sort by highest proportion first and users can reorder tags in the input to resort the priority of the population.

Admixture Proportion Plot of Selected Samples

Admixture Proportion Plot of Selected Samples

Admixture Proportion Plot of All Samples Sorted

Admixture Proportion Plot of All Samples Sorted



Package dependencies & credits

This application depends on functions contained within the RAIDS R-package. Special thanks to R packages leaflet, leaflet.extras, and Shiny.

Package dependencies:

	DBI,
	dplyr,
	DT,
	htmltools,
	leaflet,
	magrittr,
	pool,
	RSQLite,
	shiny,
	shinycssloaders

Help & feedback

For additional help or to submit feedback or bug reports, please contact:
Rebecca Hassett Cold Spring Harbor Lab hassett@cshl.edu