identify_analyte {beadplexr}

Identify analyte

Description

Identify analyte

Usage

identify_analyte(
  df,
  .parameter,
  .analyte_id,
  .column_name = "analyte",
  .k = length(.analyte_id),
  .trim = 0,
  .desc = FALSE,
  .method = c("clara", "kmeans", "dbscan", "mclust", "density_cut"),
  .data = NULL,
  ...
)

Arguments

df

A tidy data.frame.

.parameter

A character giving the name of column(s) where populations are identified.

.analyte_id

A character vector giving the ID of the analyte. The order is important and must match the expected order of analytes.

.column_name

A character giving the name of the column to store the population information.

.k

Numeric giving the number of expected clusters, or a set of initial cluster centers.

.trim

A numeric between 0 and 1, giving the fraction of points to remove by marking them NA.

.desc

A boolean to indicate if the centers of the analytes should be arranged in a descending fashion before assigning the names.

.method

A character giving the clustering method to use.

.data

Deprecated. Use df.

...

Additional arguments passed to appropriate methods, see below.

Details

This function is a wrapper around the process of:

• Finding analyte clusters

• Trimming the clusters by removing the cluster members most distant from the cluster center

• Sorting the analyte clusters based on their centers

• Giving each analyte cluster a useful name

Value

A data.frame with analyte IDs in a separate column

Additional parameters

Information on additional arguments passed, can be found here:

clara

cluster::clara()

kmeans

kmeans()

dbscan

fpc::dbscan()

mclust

mclust::Mclust()

density_cut

approx_adjust()

See Also

cluster_events()

Examples

## Not run: 
library(beadplexr)
library(ggplot2)

data("lplex")

df <- lplex[[1]]
df |>
  identify_analyte(.parameter = c("FSC-A", "SSC-A"),
                      .analyte_id = c("A", "B"),
                      .column_name = "analyte",
                      .method = "clara", .trim = 0.02) |>
  ggplot() +
  aes(x = `FSC-A`, y = `SSC-A`, colour = analyte) +
  geom_point()

df |>
  identify_analyte(.parameter = c("FSC-A", "SSC-A"),
                      .analyte_id = c("A", "B"),
                      .column_name = "analyte",
                      .method = "clara", .desc = TRUE) |>
  ggplot() +
  aes(x = `FSC-A`, y = `SSC-A`, colour = analyte) +
  geom_point()

df |>
  identify_analyte(.parameter = c("FSC-A", "SSC-A"),
                      .analyte_id = c("A", "B"),
                      .column_name = "analyte",
                      .method = "dbscan") |>
  ggplot() +
  aes(x = `FSC-A`, y = `SSC-A`, colour = analyte) +
  geom_point()

## End(Not run)