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Enhancements to Subsampling Feature in tidygate #1

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Nov 27, 2023
Merged

Enhancements to Subsampling Feature in tidygate #1

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41da432
Add subsampling feature to gate_interactive_chr_int
qclayssen Nov 19, 2023
3106cc8
add documentation for subsample
qclayssen Nov 23, 2023
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ Depends:
R (>= 3.6.0)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
RoxygenNote: 7.2.3
Imports:
utils,
graphics,
Expand Down
22 changes: 20 additions & 2 deletions R/functions_chr_int.R
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Expand Up @@ -45,6 +45,7 @@ pretty_plot_chr_int = function(.data,
.color = NULL,
.shape = NULL,
.size = NULL,
subsample = NULL,
opacity = 1,
is_size_fixed) {
# Comply with CRAN NOTES
Expand All @@ -58,8 +59,19 @@ pretty_plot_chr_int = function(.data,
.shape = enquo(.shape)
.size = enquo(.size)
my_size_range = c(1, 3)



if (!is.null(subsample)) {
if (subsample > 0 && subsample < 1) {
# Subsample as a fraction
set.seed(123) # Set seed for reproducibility
.data <- .data %>% sample_frac(subsample)
} else if (subsample >= 1) {
# Subsample as a fixed number
set.seed(123) # Set seed for reproducibility
.data <- .data %>% sample_n(subsample)
}
}


.data_formatted =
.data %>%
Expand Down Expand Up @@ -263,6 +275,7 @@ pretty_plot_chr_int = function(.data,
#' @param .color A column symbol. Color of points
#' @param .shape A column symbol. Shape of points
#' @param .size A column symbol. Size of points
#' @param subsample A numeric value or a fraction indicating the subset of data to sample.
#' @param opacity A number between 0 and 1. The opacity level of the data points
#' @param how_many_gates An integer. The number of gates to label
#' @param 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.
Expand All @@ -277,6 +290,7 @@ gate_interactive_chr_int <-
.color = NA,
.shape = NULL,
.size = NULL,
subsample = NULL,
opacity = 1,
how_many_gates = 1,
is_size_fixed,
Expand Down Expand Up @@ -336,6 +350,8 @@ gate_interactive_chr_int <-
# size can be number or column
.size = !!.size,

subsample = subsample,

opacity = opacity,
is_size_fixed = is_size_fixed
)
Expand Down Expand Up @@ -427,6 +443,7 @@ gate_programmatic_chr_int <-
.color = NULL,
.shape = NULL,
.size = NULL,
subsample = NULL,
opacity = 1,
how_many_gates = 1,
.group_by = NULL,
Expand Down Expand Up @@ -484,6 +501,7 @@ gate_programmatic_chr_int <-
.color = .color,
.shape = .shape,

subsample =subsample,
# size can be number of column
.size = .size,

Expand Down
7 changes: 7 additions & 0 deletions R/methods.R
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Expand Up @@ -16,6 +16,7 @@
#' @param .color A column symbol. Colour of points
#' @param .shape A column symbol. Shape of points
#' @param .size A column symbol. Size of points
#' @param subsample A numeric value or a fraction indicating the subset of data to sample.
#' @param opacity A number between 0 and 1. The opacity level of the data points
#' @param how_many_gates An integer. The number of gates to label
#' @param .group_by A column symbol. The column that is used to calculate distance (i.e., normally genes)
Expand Down Expand Up @@ -73,6 +74,7 @@ gate_chr <- function(.dim1,
.color = NULL,
.shape = NULL,
.size = NULL,
subsample = NULL,
opacity = 1,
how_many_gates = 1,
.group_by = NULL,
Expand All @@ -95,6 +97,7 @@ gate_chr.numeric = function( .dim1,
.color = NULL,
.shape = NULL,
.size = NULL,
subsample = NULL,
opacity = 1,
how_many_gates = 1,
.group_by = NULL,
Expand All @@ -109,6 +112,7 @@ gate_chr.numeric = function( .dim1,
.color = .color,
.shape = .shape,
.size = .size,
subsample = subsample,
opacity = opacity,
how_many_gates = how_many_gates,
.group_by = .group_by,
Expand Down Expand Up @@ -136,6 +140,7 @@ gate_int <- function(.dim1,
.color = NULL,
.shape = NULL,
.size = NULL,
subsample = NULL,
opacity = 1,
how_many_gates = 1,
.group_by = NULL,
Expand All @@ -157,6 +162,7 @@ gate_int.numeric = function( .dim1,
.color = NULL,
.shape = NULL,
.size = NULL,
subsample = NULL,
opacity = 1,
how_many_gates = 1,
.group_by = NULL,
Expand All @@ -170,6 +176,7 @@ gate_int.numeric = function( .dim1,
.color = .color,
.shape = .shape,
.size = .size,
subsample = subsample,
opacity = opacity,
how_many_gates = how_many_gates,
.group_by = .group_by,
Expand Down
11 changes: 11 additions & 0 deletions README.Rmd
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Expand Up @@ -118,4 +118,15 @@ tidygate_data %>%

```

## Subsampling

The `subsample` parameter allows you to sample a subset of your data for analysis with a fixed seed. This can be particularly useful for large datasets or for preliminary exploratory analysis. Here's how you can use it:

```{r}
# For sampling 50% of your data
result <- your_function(data, subsample = 0.5)

# For sampling 100 specific observations
result <- your_function(data, subsample = 100)

```
21 changes: 21 additions & 0 deletions README.md
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Expand Up @@ -131,3 +131,24 @@ tidygate_data %>%
## 9 adrenal 1 fibrobla… immune_c… 0.52 ACC -0.776 -0.383 0
## 10 adrenal 1 immune_c… endothel… 1 ACC 0.980 -0.116 0
## # … with 2,230 more rows

## Subsampling

The `subsample` parameter allows you to sample a subset of your data for analysis with a fixed seed. This can be particularly useful for large datasets or for preliminary exploratory analysis. Here's how you can use it:

```r
# For sampling 50% of your data
tidygate_data %>%
mutate( gate = gate_chr(
Dim1, Dim2, subsample = 0.5
))


# For sampling 100 specific observations
tidygate_data %>%
mutate( gate = gate_chr(
Dim1, Dim2, subsample = 100
))


```
4 changes: 4 additions & 0 deletions man/gate_chr-methods.Rd
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3 changes: 3 additions & 0 deletions man/gate_chr.numeric.Rd
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3 changes: 3 additions & 0 deletions man/gate_int.numeric.Rd
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3 changes: 3 additions & 0 deletions man/gate_interactive_chr_int.Rd
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