plot_SS_Simulation {BioTIP} | R Documentation

## 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.
`which2point` | A character (or integer) which state's values were used to set up the three horizontal lines. by default is NULL, indicating the values of all states will be used.

### Value

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

### Author(s)

Xinan H Yang xyang2@uchicago.edu

### 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)

[Package BioTIP version 1.1.1 Index]