identify_analyte {beadplexr} | R Documentation |
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 |
... |
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
- kmeans
- dbscan
- mclust
- density_cut
See Also
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)