plot_arc_var: Plot variance in positions, t-ratios and variance explained...

In vitkl/ParetoTI: R toolbox for Archetypal Analysis and Pareto Task Inference on single cell data

Description

plot_arc_var() shows variance in positions (total_var), t-ratios, SSE and variance explained (cumulative - varexpl, each vertex - res_varexpl) by polytope models with different number of vertices (k)

Usage

plot_arc_var(arc_data, type = c("varexpl", "SSE", "res_varexpl",
  "total_var", "t_ratio", "dim")[1], point_size = 2, line_size = 1.5,
  reorder = FALSE)

Arguments

arc_data	object of class "k_pch_fit", storing the position of vertices of best fit polytopes with different k, and other data from fit_pch() run. arc_data$XC is a list where each element is XC matrix of dim(dimensions, archetypes) storing positions of vertices with different k.
type	which measure to plot as a function of k, one of "varexpl", "SSE", "res_varexpl", "total_var", "t_ratio, "dim". Use dim to plot variance in position in each dimension.
line_size	width of lines connecting archetypes
reorder	reorder dimensions based on variance in position (type = "dim).
arch_size	size of archetype point

Value

plot_arc_var() ggplot2 (2D) plot

Author(s)

Vitalii Kleshchevnikov

See Also

fit_pch, plot_arc

Examples

library(ParetoTI)
library(ggplot2)
# Random data that fits into the triangle (2D)
set.seed(4355)
archetypes = generate_arc(arc_coord = list(c(5, 0), c(-10, 15), c(-30, -20)),
                          mean = 0, sd = 1, N_dim = 2)
data = generate_data(archetypes$XC, N_examples = 1e4, jiiter = 0.04, size = 0.9)
arc_data = k_fit_pch(data, ks = 1:4, check_installed = T, delta=0.1, order_by_side = F)
# Show polytopes and the data
plot_arc(arc_data = arc_data, data = data,
         which_dimensions = 1:2, type = "all", arch_size = 2,
         colors = c("#D62728", "#1F77B4", "#2CA02C", "#17BED0", "grey")) +
  theme_bw()
# Show variance explained by a polytope with each k
plot_arc_var(arc_data, type = c("varexpl", "SSE", "res_varexpl")[1],
             point_size = 2, line_size = 1.5) + theme_bw()

vitkl/ParetoTI documentation built on Feb. 11, 2020, 1:36 a.m.