plot_benchmark {granulator}R Documentation

Plot benchmarking analysis scores

Description

plot_benchmark plots the median correlation scores between estimated and measured cell types across methods and cell types.

Usage

plot_benchmark(benchmarked, metric = "pcc")

Arguments

benchmarked

List: output object from function benchmarked.

metric

Character: the metric of evaluation. Options include Pearson Correlation Coefficient ('pcc'), Concordance Correlation Coefficient ('ccc'), Coefficient of Determination ('adj.r2') and Root Mean Square Error ('rmse') of the linear regression model.

Value

Plot showing correlations across algorithms and cell types.

Author(s)

Vincent Kuettel, Sabina Pfister

Examples

# load demo PBMCS data
load_ABIS()

# deconvolute
decon <- deconvolute(m = bulkRNAseq_ABIS, 
sigMatrix = sigMatrix_ABIS_S0)

# bechmark
bench<- benchmark(deconvoluted = decon, 
ground_truth = groundTruth_ABIS)

# plot bechmark
plot_benchmark(benchmarked = bench, 
metric = 'pcc')


[Package granulator version 1.1.0 Index]