tidygate (version 0.4.0)

gate: DEPRECATED - use gate_chr, gate_int instead inside a dplyr::mutate() statement

Description

gate() takes as input a `tbl` formatted as | <DIMENSION 1> | <DIMENSION 2> | <...> | and calculates the rotated dimensional space of the feature value.

Usage

gate(
  .data,
  .element,
  .dim1,
  .dim2,
  .color = NULL,
  .shape = NULL,
  .size = NULL,
  opacity = 1,
  how_many_gates = 1,
  gate_list = NULL,
  name = "gate",
  action = "add",
  ...
)
# S3 method for spec_tbl_df
gate(
  .data,
  .element,
  .dim1,
  .dim2,
  .color = NULL,
  .shape = NULL,
  .size = NULL,
  opacity = 1,
  how_many_gates = 1,
  gate_list = NULL,
  name = "gate",
  action = "add",
  ...
)
# S3 method for tbl_df
gate(
  .data,
  .element,
  .dim1,
  .dim2,
  .color = NULL,
  .shape = NULL,
  .size = NULL,
  opacity = 1,
  how_many_gates = 1,
  gate_list = NULL,
  name = "gate",
  action = "add",
  ...
)

Arguments

.data

A tibble

.element

A column symbol. The column that is used to calculate distance (i.e., normally genes)

.dim1

A column symbol. The x dimension

.dim2

A column symbol. The y dimension

.color

A column symbol. Color of points

.shape

A column symbol. Shape of points

.size

A column symbol. Size of points

opacity

A number between 0 and 1. The opacity level of the data points

how_many_gates

An integer. The number of gates to label

gate_list

A list of gates. It is returned by gate function as attribute \"gate\". If you want to create this list yourself, each element of the list is a data frame with x and y columns. Each row is a coordinate. The order matter.

name

A character string. The name of the new column

action

A character string. Whether to join the new information to the input tbl (add), or just get the non-redundant tbl with the new information (get).

...

Further parameters passed to the function gatepoints::fhs

Value

A tbl object with additional columns for the inside gate information. additional columns for the rotated dimensions. The rotated dimensions will be added to the original data set as `<NAME OF DIMENSION> rotated <ANGLE>` by default, or as specified in the input arguments.

A tbl object with additional columns for the reduced dimensions. additional columns for the rotated dimensions. The rotated dimensions will be added to the original data set as `<NAME OF DIMENSION> rotated <ANGLE>` by default, or as specified in the input arguments.

A tbl object with additional columns for the reduced dimensions. additional columns for the rotated dimensions. The rotated dimensions will be added to the original data set as `<NAME OF DIMENSION> rotated <ANGLE>` by default, or as specified in the input arguments.

Details

maturing

This function allow the user to label data points in inside one or more 2D gates. This package is based on on the package gatepoints.

Examples

# NOT RUN {
# }
# NOT RUN {
  if(interactive()){

    tidygate::tidygate_data %>%
    gate( .element = c(`ct 1`, `ct 2`), Dim1, Dim2 )

  }

# }
# NOT RUN {
library(magrittr)

tidygate::tidygate_data  %>%
 gate(
   .element = c(`ct 1`, `ct 2`),
   Dim1, Dim2,
   gate_list = tidygate::gate_list
 )

# }