constellationPlot

PAC-MAN analysis result matrix that contains network annotation, clade IDs and mean (centroid) clade expression levels.

pacman_results

perplexity setting for running t-SNE

perplexity

max_iter setting for running t-SNE

max_iter

set seed to make t-SNE and consetllation plot to be reproducible

seed

plotTitle

nudge on x coordinate of centroid labels

nudge_x

nudge on y coordinate of centroid labels

nudge_y

Makes constellation plot, in which the centroids are clusters are embedded in the t-SNE 2D plane and the cross-sample relationships are plotted as lines connecting related sample clusters (clades).

Implements partition-assisted clustering and multiple alignments of networks. It 1) utilizes partition-assisted clustering to find robust and accurate clusters and 2) discovers coherent relationships of clusters across multiple samples. It is particularly useful for analyzing single-cell data set. Please see Li et al. (2017) <doi:10.1371/journal.pcbi.1005875> for detail method description.

Ye Li

Partition-Assisted Clustering and Multiple Alignments of
Networks

constellationPlot function

Makes constellation plot, in which the centroids are clusters are embedded in the t-SNE 2D plane and the cross-sample relationships are plotted as lines connecting related sample clusters (clades). — constellationPlot

Makes constellation plot, in which the centroids are clusters are embedded in the t-SNE 2D plane and the cross-sample relationships are plotted as lines connecting related sample clusters (clades).

constellationPlot: Makes constellation plot, in which the centroids are clusters are embedded in the t-SNE 2D plane and the cross-sample relationships are plotted as lines connecting related sample clusters (clades).

Description

Usage

Arguments