plot_similarity {granulator}R Documentation

Plot reference profile similariy matrix

Description

plot_similarity plots cell type similarity matrix by computing the Kendall rank correlations between cell type expression profiles. Kendall rank correlation is used to test the similarities in the ordering of data when it is ranked by quantities, and provides a less inflated measure of accuracy than Pearson correlation by accounting for ties in the data.

Usage

plot_similarity(sigMatrix)

Arguments

sigMatrix

Signature matrix: a data frame or a named list of data frames. Each signature matrix should be a genes (rows) by cell types (columns) data frame containing TPM-normalized gene expression values of signature genes.

Value

Plot showing the Kendall rank correlations similariy matrix.

Author(s)

Vincent Kuettel, Sabina Pfister

Examples

# load demo PBMCS data
load_ABIS()

# generate list of reference profiles to be tested
sigMatrix <- list(sig1 = sigMatrix_ABIS_S0, 
sig2 = sigMatrix_ABIS_S2)

# plot similarity
plot_similarity(sigMatrix = sigMatrix)


[Package granulator version 1.1.0 Index]