Results-class: Results class definition

In tchitchek-lab/SPADEVizR: SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results

Results class definition

Description

The Results object is a S4 object containing cell clustering results.

This object mainly stores the cluster abundance matrix (i.e. the number of cells associated to each sample for each cluster) and the cluster phenotypes matrix (i.e. the median expressions for each marker of each cluster).

In addition, this object can contain information about clustering results, such a SPADE tree.

Details

The 'cluster.abundances' dataframe contains the number of cells associated to each sample for each cluster. This dataframe stores the clusters in rows and the samples in columns.

The 'cluster.phenotypes' dataframe stores the median expressions for each marker of each cluster. This dataframe stores in the first column the sample names, in the second column the cluster names, and in the others columns the maker median expressions.

The 'bounds' dataframe contains the marker expressions boundaries (minimum and maximum, or specific percentiles) for each marker.

The 'print()' and 'show()' can be used to display a summary of this object.

Slots

cluster.abundances

a dataframe containing the number of cells associated to each sample for each cluster

cluster.phenotypes

a dataframe containing the median expressions for each marker of each cluster

sample.names

a character vector containing the sample names

cluster.names

a character vector containing the cluster names

cluster.number

a numeric specifying the number of clusters

marker.names

a character vector containing the marker names

clustering.markers

a character vector specifying the markers that have been used by the clustering algorithms

bounds

a numeric data.frame containing the marker expressions boundaries for each marker

trans

a character specifying what transformation ("arcsinh", "logicle", or "none") will be applied on the cluster expression matrix ("arcsinh" by default)

flowset

a flowSet object containing the imported SPADE FCS files

fcs.files

a character vector containing the location of the imported FCS files

graph

a igraph object containing the SPADE tree structure

graph.layout

a numeric matrix containing the SPADE tree layout

assignments

a dataframe containing annotations for each sample samples such as a biological condition ("bc"), a timepoint condition ("tp") or an individual ("ind") assignment

th.min_cells

a numeric specifying the minimal number of cells that a cluster for a given samples needs to have to be taken into consideration in its phenotypical characterization

tchitchek-lab/SPADEVizR documentation built on Jan. 27, 2024, 8:58 p.m.