constellationPlot {PAC}

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

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).

Usage

constellationPlot(pacman_results, perplexity, max_iter, seed,
  plotTitle = "Constellations of Clades", nudge_x = 0.3, nudge_y = 0.3)

Arguments

pacman_results

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

perplexity

perplexity setting for running t-SNE

max_iter

max_iter setting for running t-SNE

seed

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

plotTitle

max_iter setting for running t-SNE

nudge_x

nudge on x coordinate of centroid labels

nudge_y

nudge on y coordinate of centroid labels