Nothing
## -----------------------------------------------------------------------------
library(beadplexr)
library(dplyr)
library(ggplot2)
data(simplex)
## ---- fig.show='hold'---------------------------------------------------------
mplex_data <- simplex[["mplex"]]
mplex_data |>
facs_plot(.x = "FSC", .y = "SSC", .type = "hex")
mplex_data |>
facs_plot(.x = "FITC", .y = "PE", .type = "hex")
## ---- fig.show='hold'---------------------------------------------------------
cba_data <- simplex[["cba"]]
cba_data |>
facs_plot(.x = "FSC", .y = "SSC", .type = "hex")
cba_data |>
facs_plot(.x = "APC", .y = "APC-Cy7", .type = "hex")
## ---- fig.width=4-------------------------------------------------------------
mplex_analyte <- mplex_data |>
identify_analyte(.parameter = c("FITC", "PE"), .analyte_id = as.character(c(1:10)))
mplex_analyte |>
facs_plot(.x = "FITC", .y = "PE", .beads = "analyte")
mplex_analyte <- mplex_data |>
identify_analyte(.parameter = c("FITC", "PE"), .analyte_id = as.character(c(1:10)), .trim = 0.1)
mplex_analyte |>
facs_plot(.x = "FITC", .y = "PE", .beads = "analyte")
## ---- fig.width=5, fig.height=3-----------------------------------------------
mplex_analyte |>
filter(!is.na(analyte)) |>
mutate(analyte = factor(analyte, levels = c(1:10))) |>
ggplot() +
aes(x = APC, fill = analyte) +
geom_density()+
facet_wrap(~ analyte)+
theme(legend.position = "none")
## ---- fig.width=5, fig.height=3-----------------------------------------------
mplex_analyte |>
# filter(!is.na(analyte)) |>
group_by(analyte) |>
trim_population(.parameter = "APC", .column_name = "analyte", .trim = 0.05) |>
ungroup() |>
mutate(analyte = factor(analyte, levels = c(1:10))) |>
ggplot() +
aes(x = APC, fill = analyte) +
geom_density() +
facet_wrap(~ analyte) +
theme(legend.position = "none")
## ---- fig.width=5, fig.height=4-----------------------------------------------
cba_analyte <- cba_data |>
identify_analyte(.parameter = c("APC", "APC-Cy7"), .analyte_id = as.character(c(1:30)), .trim = 0.1)
cba_analyte |>
facs_plot(.x = "APC", .y = "APC-Cy7", .beads = "analyte")
## -----------------------------------------------------------------------------
mplex_analyte |>
filter(!is.na(analyte)) |>
group_by(analyte) |>
summarise(`FITC mean` = mean(FITC), `PE mean` = mean(PE)) |>
arrange(`FITC mean`, `PE mean`) |>
knitr::kable()
## ---- warning=FALSE, fig.width=5, fig.height=4--------------------------------
cba_analyte <- cba_data |>
despeckle(.parameter = c("APC", "APC-Cy7"), .neighbours = 2) |>
identify_analyte(.parameter = c("APC", "APC-Cy7"), .analyte_id = as.character(c(1:30)), .trim = 0.01)
cba_analyte |>
facs_plot(.x = "APC", .y = "APC-Cy7", .beads = "analyte")
## ----results='markup',echo=FALSE----------------------------------------------
sessionInfo()
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