flowGraph-class: 'flowGraph': A class for storing cell count feature values...

In aya49/flowGraph: Identifying differential cell populations in flow cytometry data accounting for marker frequency

'flowGraph': A class for storing cell count feature values for the Phenotype class.

Description

'flowGraph': A class for storing cell count feature values for the Phenotype class.

Usage

## S4 method for signature 'flowGraph'
show(object)

Arguments

object

A flowGraph object.

Value

a flowGraph object.

Methods (by generic)

• show: show method

Slots

feat

A list containing elements node and edge, each containing a list with feature values; each element in this list is named by the feature name and contains a numeric matrix with the sample id's as row names and cell populations phenotype labels or edge labels as column names. Column names for edge features are labelled as <from>_<to> e.g. A+_A+B+.

feat_desc

A list containing elements node and edge, each containing a data frame describing the features in the feat slot with columns:

• feat: feature name.

• nrow: number of samples.

• ncol: number of nodes or edges.

• inf: number of infinite values in the matrix.

• neginf: number of negative infinite values in the matrix.

• na: number of NA values in the matrix.

• nan: number of NaN values in the matrix.

• neg: number of negative values in the matrix.

• pos: number of positive values in the matrix.

• zero: number of 0's in the matrix.

• max: The maximum value in the matrix.

• min: The minimum value in the matrix.

summary

A list containing elements node and edge, each containing a list with a feature summary list; each feature summary in this list contains elements:

• values: a numeric vector the same length as the number of nodes or edges.

• test_custom: a function or a string name of the summary test method used.

summary_desc

A list containing elements node and edge, each containing a data frame describing the features in feat with columns:

• feat: A string indicating feature name the summary was created for.

• test_name: A string containing the name of the summary.

• class: A string corresponding to the column name of the meta slot whose values represent the class label of each sample on which the summary was created to compare or analyze.

• label1: A string from the class column of the meta slot indicating one of the labels compared to create the summary statistic.

• label2: A string from the class column of the meta slot indicating one of the labels compared to create the summary statistic.

meta

A data frame containing the column(s) id (sample id's corresponding to row names of features in the feat slot) and any other meta data pertaining to samples being analyzed.

markers

A character vector containing markers used.

edge_list

A list containing elements child and parent. These elements contain an edge list from child to parent and vice versa.

graph

A list containing data frames v and e with information on cell population nodes and edges. v contains columns:

• phenotype: The cell population node label names e.g. A+B+C+.

• phenocode: A string of "0", "1", "2", ... indicating the whether each marker is expressed on a cell population.

• phenolayer: The layer on which a cell population resides i.e. the numer of markers in its phenotype label.

• phenogroup: The markers used the make up the phenotype.

plot_layout

A string indicating the name of the igraph layout function used to layout the cell population nodes for plotting.

etc

A list containing other information (see fg_get_summary for other things stored in this slot):

• cumsumpos: A logical indicating whether cell counts in flowGraph object contains cumulated cell counts; this is optional and can be done only for there is more than one threshold for one or more markers. This should also only be ran when initializing a flowGraph object as converting back and forth is computationally expensive. If the user is interested in seeing non- and cumulated counts, we recommend keeping two flowGraph objects, one for each version. This function simply converts e.g. the count of A+ or A++ into the sum of count of A+, A++, and A+++ or A++, and A+++.

• class_mean_normalized: A logical indicating whether the features in the flowGraph object has been normalized according to some sample meta e.g. subject.

• save: A list containing a string indicating the save ID of the object and a string indicating path where the object is saved – used in function save_fg to identify whether or not to save to the same folder.

Creating Objects

Objects can be created using new("flowFrame") or the constructor flowGraph, with mandatory argument input_. Creating objects using new is discouraged.

Methods

'object' represents a flowGraph object.

• show(fg): Shows a description of the flowGraph object.

• fg_get_meta: Retrieves the sample meta data from a given flowGraph object. See fg_get_meta.

• fg_get_graph: Retrieves the cell population (v) and edge (e) meta data from a given flowGraph object. See fg_get_graph.

• fg_get_feature: Retrieves the numeric feature matrix requested by the user from a given flowGraph object. See fg_get_feature.

• fg_get_summary: Retrieves the feature summary list requested by the user from a given flowGraph object. See fg_get_summary.

• fg_get_feature_desc: Retrieves the data frame from the feat_desc slot of a given flowGraph object. See fg_get_feature_desc.

• fg_get_summary_desc: Retrieves the data frame from the summary_desc slot of a given flowGraph object. See fg_get_summary_desc.

• fg_add_feature: Adds a feature to a given flowGraph object; we do not recommend users directly use this method, instead please use wrapper functions e.g. fg_feat_node_prop, fg_feat_node_specenr, See fg_add_feature.

• fg_rm_feature: Removes a user specified feature from a given flowGraph object. See fg_rm_feature.

• fg_add_summary: Adds a feature to a given flowGraph object; we do not recommend users directly use this method, instead please use wrapper function fg_summary.

• fg_clear_summary: Removes all feature summaries from a given flowGraph object. See fg_clear_summary.

• fg_rm_summary: Removes a user specified feature summaries from a given flowGraph object. See fg_rm_summary.

• fg_gsub_markers: Substitutes marker names in a given flowGraph object. See fg_gsub_markers.

• fg_gsub_ids: substitutes sample id's in a flowGraph object See fg_gsub_ids.

• fg_merge_samples: Merges the samples of two flowGraph objects; we recomment users use the wrapper function fg_merge instead. See fg_merge_samples.

• fg_extract_samples: Extract data for specific samples from a flowGraph object. See fg_extract_samples.

• fg_extract_phenotypes: Extract data for specific cell population nodes from a flowGraph object. See fg_extract_phenotypes.

• fg_merge: Merges two given flowGraph objects. See fg_merge.

• fg_set_layout: Sets layout for cell population nodes for the purpose of plotting. See fg_set_layout.

• fg_plot: Plots cell hierarchies in the flowGraph object. See fg_plot.

Examples

 showClass("flowGraph")

aya49/flowGraph documentation built on Feb. 4, 2024, 6:40 p.m.