WhatIs: Inspect a specific cluster or annotated population

In davnovak/SingleBench: Framework for benchmarking and optimising dimension-reduction and clustering pipelines in expression data analysis

Description

For a select group of cells (cluster or annotated population), signal intensiry for each parameter (marker) is plotted, as well as the heatmap of inter-parameter Spearman correlations. If there are multiple clusters or populations, these plots are generated for all of them.

Usage

WhatIs(
  benchmark,
  idx.subpipeline = NULL,
  idx.n_param = NULL,
  idx.run = 1,
  cluster = NULL,
  population = NULL,
  pointsize = 0.1
)

Arguments

benchmark	object of type Benchmark
idx.subpipeline	integer: index of subpipeline (if a cluster is to be retrieved). Default value is NULL
idx.n_param	integer: n-parameter iteration index (if a cluster is to be retrieved and n-parameter was specified in the benchmark set-up). Default value is NULL
idx.run	integer: which clustering run to use if clustering was run repeatedly. Default value is 1
cluster	integer or integer vector: index (indices) of cluster of interest (if a cluster is to be retrieved). Default value is NULL
population	string or string vector: name (names) of population of interest (if a population is to be retrieved). Default value is NULL
pointsize	numeric: size of points in expression scatter plot. Default value is 0.1

davnovak/SingleBench documentation built on Dec. 19, 2021, 9:10 p.m.