plot_SS_Simulation: Density plot the leading two distance between any two states...

In xyang2uchicago/NPS: BioTIP: An R package for characterization of Biological Tipping-Point

Density plot the leading two distance between any two states from random scores of all states in a system.

Description

Generate a density plot of Ic score (orBioTIP score) from a simulation, which is the distance between the first-larget and the second-largest random scores. This is an alternative method to estimate the significance of an observed BioTIP (or Ic) score in a system. This measurement makes more sense to evaluate random scores of sample-label shuffling, in which the nature sample-sample correlation within a phenotypic state (or cell subpopulation) was removed.

Usage

plot_SS_Simulation(
  Ic,
  simulation,
  las = 0,
  xlim = NULL,
  ylim = NULL,
  order = NULL,
  main = "1st max - 2nd max",
  ylab = "1st max - 2nd max"
)

Arguments

Ic	A vector with names of states. If order is not assigned, then plot by the order of this vector.
simulation	A numeric matrix of Ic scores in which rows are states and columns are numbers of simulated times. It can be obtained from simulation_Ic
las	Numeric in 0, 1, 2, 3; the style of axis labels. Default is 0, meaning labels are parallel. (link to http://127.0.0.1:21580/library/graphics/html/par.html).
xlim	An integer vector of length 2. Default is NULL.
ylim	An integer vector of length 2. Default is NULL.
order	Characters of names of Ic to be plotted in a desired order. Default is NULL.
main	A character vector. The title of the plot. Default is NULL.
ylab	titles y axes, as in plot.

Value

Return a plot of the observed Ic (red) and simulated Ic (grey) scores per state.

Author(s)

Xinan H Yang [e-mail]

Examples

sim = matrix(sample(1:10, 9), 3, 3)
row.names(sim) = paste0('state', 1:3)
Ic = c('state1' = 3.4, 'state2' = 15.6, 'state3' = 2)
plot_SS_Simulation(Ic, sim)

xyang2uchicago/NPS documentation built on June 30, 2024, 10:15 p.m.