Gate-class: CITEViz Gate Class

In maxsonBraunLab/CITE-Viz: "CITEViz: Classifying Cell Clusters in CITE-Seq Data using the Flow Cytometry Gating Workflow"

CITEViz Gate Class

Description

The Gate class is the core data structure of CITEViz to store gating information. Gates are initiated upon the first click of the "Gate" button and turned into a reactive value to facilitate interactivity with R-Shiny. The Gate class holds the following information:

* counter <integer>: keep track of gate number * assay_name <character>: keep track of which assay (RNA, ADT, etc) the gate data is coming from * input_cells <list>: a list of cell barcodes going into the gate e.g. if a gate isn't initialized yet, this variable contains all the cells. * input_coords <data.frame>: the coordinates of the input cells * subset_cells <list>: a list of output cells * subset_coords <data.frame>: the coordinates of the output cells * x_axis <character>: the feature used to plot the x-axis * y_axis <character>: the feature used to plot the y-axis * gate_coords <list>: the coordinates of the gate boundaries drawn by plotly * name_subset_cells <character>: the label of the set of output cells inputted by the user * num_input_cells <integer>: number of input cells * num_subset_cells <integer>: number of output cells * total_num_cells_in_sample <integer>: total number of cell in a sample * pct_subset_from_previous <numeric>: proportion of output cell WRT previous gate * pct_subset_from_total <numeric>: proportion of output cell WRT total cells

Value

a gate class object

Slots

counter

<integer>: keep track of gate number

assay_name

<character>: keep track of which assay (RNA, ADT, etc) the gate data is coming from

input_cells

<list>: a list of cell barcodes going into the gate e.g. if a gate isn't initialized yet, this variable contains all the cells.

input_coords

<data.frame>: the coordinates of the input cells

subset_cells

<list>: a list of output cells

subset_coords

<data.frame>: the coordinates of the output cells

x_axis

<character>: the feature used to plot the x-axis

y_axis

<character>: the feature used to plot the y-axis

gate_coords

<list>: the coordinates of the gate boundaries drawn by plotly

name_subset_cells

<character>: the label of the set of output cells inputted by the user

num_input_cells

<integer>: number of input cells

num_subset_cells

<integer>: number of output cells

total_num_cells_in_sample

<integer>: total number of cell in a sample

pct_subset_from_previous

<numeric>: proportion of output cell WRT previous gate

pct_subset_from_total

<numeric>: proportion of output cell WRT total cells

maxsonBraunLab/CITE-Viz documentation built on Oct. 26, 2023, 9:52 p.m.