identify_assay_analyte | R Documentation |
Convenience functions to identify analytes in different multiplex systems.
identify_legendplex_analyte(df, .analytes, .method_args, .data = NULL)
identify_cba_analyte(
df,
.analytes,
.method_args,
.trim_fs = NULL,
.parameter_fs = NULL,
.data = NULL
)
identify_macsplex_analyte(
df,
.analytes,
.method_args,
.trim_fs = NULL,
.parameter_fs = NULL,
.data = NULL
)
df |
A tidy data.frame. |
.analytes |
A vector or list giving the IDs of the analytes. The order is important and must match the expected order of analytes. |
.method_args |
A list giving the parameters passed on to |
.data |
Deprecated. Use |
.trim_fs |
A numeric between 0 and 1, giving the fraction of points to remove from the forward side scatter. |
.parameter_fs |
A character giving the names of the forward and side scatter parameters. |
These functions wraps around the process of:
Trim or subset on forward side scatter
Identifying analytes. For LEGENDplex in both bead groups
If the forward side scatter events are not trimmed, the function is equivalent
to call identify_analyte()
with CBA or MACSPlex data.
A data.frame
The parameter .analytes
is either a simple vector with the IDs or, in the
case of the LEGENDplex system, a list giving the IDs of analytes among the groups A and B.
A list for the LEGENDplex system might look like this:
list(A = c("A1", "A2"), B = c("B1", "B2"))
The order of analyte IDs is important and must match the expected order of analytes.
The parameter .method_args
is a list of key-value pairs passed to identify_analyte()
.
## Not run:
library(beadplexr)
library(dplyr)
data("lplex")
df <- lplex[[1]]
panel_info <- load_panel(.panel_name = "Human Growth Factor Panel (13-plex)")
args_ident_analyte <- list(fs = list(.parameter = c("FSC-A", "SSC-A"),
.column_name = "Bead group",
.trim = 0.1,
.method = "clara"),
analytes = list(.parameter = "FL6-H",
.column_name = "Analyte ID",
.trim = 0,
.method = "clara"))
annot_events <- identify_legendplex_analyte(df = df,
.analytes = panel_info$analytes,
.method_args = args_ident_analyte)
annot_events |> facs_plot(.beads = "Bead group")
annot_events |>
filter(`Bead group` == "A") |>
facs_plot(.x = "FL2-H", .y = "FL6-H", .beads = "Analyte ID")
annot_events |>
filter(`Bead group` == "B") |>
facs_plot(.x = "FL2-H", .y = "FL6-H", .beads = "Analyte ID")
## End(Not run)
## Not run:
library(beadplexr)
data(simplex)
df <- simplex[["cba"]]
analytes <- vector("list", 30) |> setNames(as.character(c(1:30)))
args_ident_analyte <- list(.parameter = c("APC", "APC-Cy7"),
.column_name = "Analyte ID",
.trim = 0.1,
.method = "clara")
annot_events <- identify_cba_analyte(df = df,
.analytes = analytes,
.method_args = args_ident_analyte)
annot_events |> facs_plot(.x = "FSC", .y = "SSC")
annot_events |>
facs_plot(.x = "APC", .y = "APC-Cy7", .beads = "Analyte ID")
annot_events <- identify_cba_analyte(df = df,
.analytes = analytes,
.method_args = args_ident_analyte,
.trim_fs = 0.1,
.parameter_fs = c("FSC", "SSC"))
annot_events |> facs_plot(.x = "FSC", .y = "SSC", .beads = "Bead events")
# Looks strange because some true beads events have randomly been placed far
# from the center in the forward-side scatter when the data was created
annot_events |>
facs_plot(.x = "APC", .y = "APC-Cy7", .beads = "Analyte ID")
## End(Not run)
## Not run:
library(beadplexr)
data(simplex)
df <- simplex[["mplex"]]
analytes <- vector("list", 10) |> setNames(as.character(c(1:10)))
args_ident_analyte <- list(.parameter = c("FITC", "PE"),
.column_name = "Analyte ID",
.trim = 0.1,
.method = "clara")
annot_events <- identify_macsplex_analyte(df = df,
.analytes = analytes,
.method_args = args_ident_analyte)
annot_events |> facs_plot(.x = "FSC", .y = "SSC")
annot_events |>
facs_plot(.x = "FITC", .y = "PE", .beads = "Analyte ID")
annot_events <- identify_macsplex_analyte(df = df,
.analytes = analytes,
.method_args = args_ident_analyte,
.trim_fs = 0.1,
.parameter_fs = c("FSC", "SSC"))
annot_events |> facs_plot(.x = "FSC", .y = "SSC", .beads = "Bead events")
# Looks strange because some true beads events have randomly been placed far
# from the center in the forward-side scatter when the data was created
annot_events |>
facs_plot(.x = "FITC", .y = "PE", .beads = "Analyte ID")
## End(Not run)
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