Type: Package
Title: Interactively Gate Points
Version: 1.0.14
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Description: Interactively gate points on a scatter plot. Interactively drawn gates are recorded and can be applied programmatically to reproduce results exactly. Programmatic gating is based on the package gatepoints by Wajid Jawaid (who is also an author of this package).
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.1
Depends: R (≥ 3.6.0)
Imports: utils, graphics, lifecycle, scales, magrittr, tibble, dplyr, purrr, rlang, tidyr, viridis, grDevices, RColorBrewer, stringr, shiny, plotly, ggplot2
RdMacros: lifecycle
Suggests: testthat, markdown, knitr, readr
VignetteBuilder: knitr
Biarch: true
biocViews: AssayDomain, Infrastructure
URL: https://github.com/stemangiola/tidygate
BugReports: https://github.com/stemangiola/tidygate/issues
NeedsCompilation: no
Packaged: 2024-09-17 19:33:12 UTC; a1234450
Author: Stefano Mangiola [aut, cre], Wajid Jawaid [ctb], William Hutchison ORCID iD [aut]
Repository: CRAN
Date/Publication: 2024-09-17 19:50:02 UTC

Add attribute to abject

Description

Add attribute to abject

Usage

add_attr(var, attribute, name)

Arguments

var

A tibble

attribute

An object

name

A character name of the attribute

Value

A tibble with an additional attribute

Demo gate data

Description

Demo gate data

Usage

demo_gate_data

Format

An object of class tbl_df (inherits from tbl, data.frame) with 26 rows and 3 columns.

Freehand select

Description

Freehand select

Usage

fhs(data, mark = TRUE, names = TRUE, ...)

Arguments

data

Data frame or matrix of co-ordinates. (x,y) co-ordinates for each point will be on rows. Rownames of selected points will be returned.

mark

Default TRUE. Predicate marking of selected points.

names

Default TRUE. If TRUE will return rownames of data frame with points within polygon. If FALSE will return logical vector.

...

Additional parameters passed to points.

Details

Freehand select function. First generate a 2D plot using R's plot function, then select gate region by left clicking. Close polygon by right clicking. The function will return the rownames of the enclosed points by the rownames of th co-ordinates given in data.

Value

Returns character vector of rownames of the selected points from data if names parameter is TRUE. If names is FALSE then a logical vector indicating whether points are in the polygon is returned.

Author(s)

Wajid Jawaid

Examples

if(interactive()) {
  x <- cbind(1:10, 1:10)
  rownames(x) <- 1:10
  plot(x, pch = 16, col = "red")
  fhs(x)
}

Gate points

Description

Gate points based on their X and Y coordinates. By default, this function launches an interactive scatter plot. Colour, shape, size and alpha can be defined as constant values, or can be controlled by the values of a specified column.

If previously drawn gates are supplied to the 'programmatic_gates' argument, points will be gated programmatically. This feature allows the reproduction of previously drawn interactive gates. Programmatic gating is based on the package gatepoints by Wajid Jawaid.

Usage

gate(
  x,
  y,
  colour = NULL,
  shape = NULL,
  alpha = 1,
  size = 2,
  programmatic_gates = NULL
)

Arguments

x

A vector representing the X dimension.

y

A vector representing the Y dimension.

colour

A single colour code string compatible with ggplot2. Or, a vector representing the point colour.

shape

A single ggplot2 shape numeric ranging from 0 to 127. Or, a vector representing the point shape, coercible to a factor of 6 or less levels.

alpha

A single ggplot2 alpha numeric ranging from 0 to 1. Or, a vector representing the point alpha, either a numeric or factor of 6 or less levels.

size

A single ggplot2 size numeric ranging from 0 to 20. Or, a vector representing the point size, either a numeric or factor of 6 or less levels.

programmatic_gates

A 'data.frame' of the gate brush data, as saved in 'tidygate_env$gates'. The column 'x' records X coordinates, the column 'y' records Y coordinates and the column '.gate' records the gate number. When this argument is supplied, gates will be drawn programmatically.

Value

A vector of strings, of the gates each X and Y coordinate pair is within. If gates are drawn interactively, they are temporarily saved to 'tidygate_env$gates'.

Examples

library(dplyr)
data("demo_gate_data", package = "tidygate")

# Gate points interactively
if(interactive()) {
  mtcars |>
    mutate(gated = gate(x = mpg, y = wt, shape = am))
}

# Gate points programmatically
mtcars |>
  mutate(gated = gate(x = mpg, y = wt, programmatic_gates = demo_gate_data))

Label points within a scatter plot drawing a gate

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_chr(
  .dim1,
  .dim2,
  .color = NULL,
  .shape = NULL,
  .size = NULL,
  opacity = 1,
  how_many_gates = 1,
  .group_by = NULL,
  gate_list = NULL,
  ...
)

gate_int(
  .dim1,
  .dim2,
  .color = NULL,
  .shape = NULL,
  .size = NULL,
  opacity = 1,
  how_many_gates = 1,
  .group_by = NULL,
  gate_list = NULL,
  ...
)

Arguments

.dim1

A column symbol. The x dimension

.dim2

A column symbol. The y dimension

.color

A column symbol. Colour 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

.group_by

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

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.

...

Further parameters passed to the function gatepoints::fhs

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.

Value

An character vector, with "0" for elements outside gates and "1..N" for the elements inside the N gates.

An integer vector, with 0 for elements outside gates and 1..N for the elements inside the N gates.

Examples


# Standard use - interactive

if(interactive()){

  tidygate::tidygate_data  %>%
    distinct(`ct 1` , `ct 2`, Dim1, Dim2) %>%
    mutate(gate = gate_chr( Dim1, Dim2)) 

}

library(magrittr)
library(dplyr)

# Standard use - programmatic
res_distinct =
 tidygate::tidygate_data  %>%
 distinct(`ct 1` , `ct 2`, Dim1, Dim2) %>%
 mutate(gate = gate_chr( Dim1, Dim2,gate_list = tidygate::gate_list)) 

# Grouping - programmatic
res =
 tidygate::tidygate_data  %>%
   mutate(gate = gate_chr( 
     Dim1, Dim2,
     .group_by = c(`ct 1` , `ct 2`), 
     gate_list = tidygate::gate_list
   ))

gate_chr

Description

gate_chr

Usage

## S3 method for class 'numeric'
gate_chr(
  .dim1,
  .dim2,
  .color = NULL,
  .shape = NULL,
  .size = NULL,
  opacity = 1,
  how_many_gates = 1,
  .group_by = NULL,
  gate_list = NULL,
  ...
)

Arguments

.dim1

A column symbol. The x dimension

.dim2

A column symbol. The y dimension

.color

A column symbol. Colour 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

.group_by

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

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.

...

Further parameters passed to the function gatepoints::fhs

Value

An character vector, with "0" for elements outside gates and "1..N" for the elements inside the N gates.

gate_int

Description

gate_int

Usage

## S3 method for class 'numeric'
gate_int(
  .dim1,
  .dim2,
  .color = NULL,
  .shape = NULL,
  .size = NULL,
  opacity = 1,
  how_many_gates = 1,
  .group_by = NULL,
  gate_list = NULL,
  ...
)

Arguments

.dim1

A column symbol. The x dimension

.dim2

A column symbol. The y dimension

.color

A column symbol. Colour 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

.group_by

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

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.

...

Further parameters passed to the function gatepoints::fhs

Value

An integer vector, with 0 for elements outside gates and 1..N for the elements inside the N gates.

Interactively gate data with a simple scatter plot

Description

Create an interactive scatter plot based on user-defined X and Y coordinates. Colour, shape, size and alpha can be defined as constant values, or can be controlled by values in a specified column.

Usage

gate_interactive(x, y, colour = NULL, shape = NULL, alpha = 1, size = 2)

Arguments

x

A vector representing the X dimension.

y

A vector representing the Y dimension.

colour

A single colour code string compatible with ggplot2. Or, a vector representing the point colour.

shape

A single ggplot2 shape numeric ranging from 0 to 127. Or, a vector representing the point shape, coercible to a factor of 6 or less levels.

alpha

A single ggplot2 alpha numeric ranging from 0 to 1. Or, a vector representing the point alpha, either a numeric or factor of 6 or less levels.

size

A single ggplot2 size numeric ranging from 0 to 20. Or, a vector representing the point size, either a numeric or factor of 6 or less levels.

Value

A vector of strings, of the gates each X and Y coordinate pair is within. If gates are drawn interactively, they are temporarily saved to 'tidygate_env$gates'

Get points within a user drawn gate

Description

Get points within a user drawn gate

Usage

gate_interactive_chr_int(
  .data,
  .dim1,
  .dim2,
  .color = NA,
  .shape = NULL,
  .size = NULL,
  opacity = 1,
  how_many_gates = 1,
  is_size_fixed,
  ...
)

Arguments

.data

A tibble

.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

...

Further parameters passed to the function gatepoints::fhs

Value

A tibble with additional columns

Get points within a user drawn gate

Description

Get points within a user drawn gate

Usage

gate_interactive_old(
  .data,
  .element,
  .dim1,
  .dim2,
  .color = NULL,
  .shape = NULL,
  .size = NULL,
  opacity = 1,
  how_many_gates = 1,
  name = "gate",
  ...
)

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

name

A character string. The name of the new column

...

Further parameters passed to the function gatepoints::fhs

Value

A tibble with additional columns

Example gate_list

Description

Example gate_list

Usage

gate_list

Format

An object of class list of length 2.

Programmatically gate data with pre-recorded lasso selection coordinates

Description

A helpful way to repeat previous interactive lasso selections to enable reproducibility. Programmatic gating is based on the package [gatepoints](https://github.com/wjawaid/gatepoints) by Wajid Jawaid.

Usage

gate_programmatic(x, y, programmatic_gates)

Arguments

x

A vector representing the X dimension.

y

A vector representing the Y dimension.

programmatic_gates

A 'data.frame' of the gate brush data, as saved in 'tidygate_env$gates'. The column 'x' records X coordinates, the column 'y' records Y coordinates and the column '.gate' records the gate number.

Value

A vector of strings, of the gates each X and Y coordinate pair is within.

Get points within a user drawn gate

Description

Get points within a user drawn gate

Usage

gate_programmatic_chr_int(.data, .dim1, .dim2, gate_list, ...)

Arguments

.data

A tibble

.dim1

A column symbol. The x dimension

.dim2

A column symbol. The y dimension

gate_list

A list of gates. Each element of the list is a data frame with x and y columns. Each row is a coordinate. The order matter.

...

Further parameters passed to the function gatepoints::fhs

Value

A tibble with additional columns

Get points within a user drawn gate

Description

Get points within a user drawn gate

Usage

gate_programmatic_old(
  .data,
  .element,
  .dim1,
  .dim2,
  gate_list,
  name = "gate",
  ...
)

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

gate_list

A list of gates. 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

...

Further parameters passed to the function gatepoints::fhs

Value

A tibble with additional columns

Convert array of quosure (e.g. c(col_a, col_b)) into character vector

Description

Convert array of quosure (e.g. c(col_a, col_b)) into character vector

Convert array of quosure (e.g. c(col_a, col_b)) into character vector

Usage

quo_names(v)

quo_names(v)

Arguments

v

A array of quosures (e.g. c(col_a, col_b))

Value

A character vector

A character vector

Run Shiny App for interactive gating

Description

Run Shiny App for interactive gating

Usage

server(input, output, session)

Arguments

input

Server input parameter

output

Server output parameter

session

Server session parameter

Value

NA

Example data set

Description

Example data set

Usage

tidygate_data

Format

An object of class spec_tbl_df (inherits from tbl_df, tbl, data.frame) with 2240 rows and 8 columns.

Create Shiny App UI

Description

Create Shiny App UI

Usage

ui

Format

An object of class shiny.tag.list (inherits from list) of length 4.

Value

Fluid UI container