flowGraph-class {flowGraph} | R Documentation

## '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")

[Package flowGraph version 1.2.0 Index]