show_reduced_space: show_reduced_space

In charles-bernard/mage: Mine Associated Gene Expressions (from single-cell Rna Seq data)

Description

Reduce the space of the scores to its first principal components in order to display on it the associated gene pairs.

Usage

show_reduced_space(x, x_ixs = NULL, partition = NULL,
  partition_ixs = NULL, PCs = 1:4, output_dir = NULL)

Arguments

x	data.frame; the table of scores
x_ixs	(optional) list containing a unique n-by-m matrix of boolean indexes resulting from the sample function where n is the number of individuals in x and m is the number of methods used for the sampling
partition	(optional) vector; partition of x into k clusters
partition_ixs	(optional) list of n-by-m matrices of boolean indexes resulting from sample function where n is the number of individuals in a given cluster of the partition and m is is the number of methods used for the sampling
PCs	numeric vector of Principal Compenents to be considered (max = 5)
output_dir	(optional) path to a directory where to store all the plots

Details

the function show_reduced_space returns a graphical object composed of 2 up to 5 elements:

PCA_information

The graphical informations about the PCA

population

Show all the gene pairs in the reduced space

population_samples

Show the sampled gene pairs within the population (ixs must be provided)

clusters

Show the different clusters of the population (partition must be provided)

clusters_samples

Show the different sampled gene pairs within each clusters (partition_ixs must be provided)

Value

Returns a list of plots

charles-bernard/mage documentation built on May 14, 2019, 2 a.m.