ks.test_expl: simulation and plots explaining KS-test and Wilcox-test

In vitkl/regNETcmap: Tools to study transcriptional regulation using perturbation screens followed by transcriptomic profiling (incl. CMAP, Perturb-seq)

Description

This function generates random data (rnorm, or other provided by distr argument) or uses user-provided data to explain how KS-test and Wilcox-test measure difference in distributions. It shows empirical cumulative distribution of z-scores for a given group of genes (set) and for all other genes (other). User can compare this plot to the KS-test and the Wilcox-test results.

Usage

ks.test_expl(N_other = 1000, N_set = 100, alternative = "greater",
  z_score = 1.5, prop_pos = 0.3, prop_neg = 0, x_coor_other = -1.7,
  x_coor_set = 1.7, cex = 1.7,
  title = "Treatment: anti-Oct4 shRNA.\nOct4 is a pos. and a neg. regulator of its targets",
  xlab = "z-score, simulated", lab_other = "other genes",
  lab_set = "Oct4 targets", seed = 1, x = NULL, y = NULL,
  gener_dist = NULL, gener_dist_lab = "all genes", distr = rnorm,
  col_other = "black", col_set = "blue", ...)

Arguments

N_other	integer, size of the "other" group, ignored if x is provided
N_set	integer, size of the "set" group, ignored if y is provided
alternative	character, "greater" or "less". The choice of alternative hypothesis for KS-test ks.test. Greater tests is the set (y) distribution (or, in case of Wilcox test, it's median) is shifted to the right compated to other (x) distribution. This choice of "greater" or "less" is flipped for the Wilcox test due to difference in the null hypothesis formulation (wilcox.test).
z_score	numeric, size of the true difference
prop_pos	numeric, between 0 and 1, the fraction of "set" group that is higher than other by z_score
prop_neg	numeric, between 0 and 1, the fraction of "set" group that is lower than other by z_score
x_coor_other	numeric, x coordinate of "other" group label on the plot
x_coor_set	numeric, x coordinate of "set" group label on the plot
cex	numeric, plotting parameter, size of the group label text, axis label text and axis annotation text
title	character, title of the plot
xlab	character, x-axis label
lab_other	character, other group label
lab_set	character, set group label
seed	integer, to initialise random number generator for reproducibility
x	numeric vector, the distribution of values of the "other" group. These can come from the experimental data.
y	numeric vector, the distribution of values of the "set" group. These can come from the experimental data.
distr	function that generates a vector of random numbers of lenght n (n argument to this function). rnorm by default
col_other	color of the other distribution (passed to plot(col = )). Details plot
col_set	color of the other distribution (passed to plot(col = )). Details plot
...	other plotting parameters plot

Value

list containing the output of KS-test and Wilcox-test

Author(s)

Vitalii Kleshchevnikov

Examples

# Let's have a look at a TF that regulates
# some of it's targets positively, some negatively and some are not affected.
ks.test_expl(alternative = "greater", prop_pos = 0.33, prop_neg = 0.4, seed = 1, cex.main = 1.4)

vitkl/regNETcmap documentation built on Feb. 18, 2020, 3:43 a.m.