## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
options(rmarkdown.html_vignette.check_title = FALSE)
setup <- function() {
  needed <- c("knitr", "rmarkdown", "tidyverse", "kableExtra")
  
  lapply(needed, function(pkg) {
    if (requireNamespace(pkg, quietly = TRUE)) {
      library(pkg, character.only = TRUE)
    }
  })
}

setup()
library(SeroTrackR)

## ----setup pk analysis, eval=FALSE--------------------------------------------
# library(SeroTrackR)
# library(tidyverse)

## -----------------------------------------------------------------------------
your_raw_data_5std <- c(
  system.file("extdata", "example_MAGPIX_pk_5std_plate1.csv", package = "SeroTrackR"),
  system.file("extdata", "example_MAGPIX_pk_5std_plate2.csv", package = "SeroTrackR")
)
your_plate_layout_5std <- system.file("extdata", "example_platelayout_pk_5std.xlsx", package = "SeroTrackR")

## -----------------------------------------------------------------------------
results_5stdcurve <- runPlasmoPipeline(
  raw_data = your_raw_data_5std,
  platform = "magpix",
  plate_layout = your_plate_layout_5std,
  panel = "panel1",
  std_point = 5, 
  experiment_name = "5-point standard curve"
)

## -----------------------------------------------------------------------------
results_5stdcurve$std_curve

## -----------------------------------------------------------------------------
results_5stdcurve$bead_counts

## -----------------------------------------------------------------------------
results_5stdcurve$blanks

## -----------------------------------------------------------------------------
results_5stdcurve$mfi_outputs$All_Results %>%
  head() %>% 
  kable()

## -----------------------------------------------------------------------------
results_5stdcurve$mfi_outputs$MFI_RAU %>%
  head() %>% 
  kable()

## -----------------------------------------------------------------------------
results_5stdcurve$mfi_outputs$MFI_RAU_long %>%
  head() %>% 
  kable()

## -----------------------------------------------------------------------------
your_raw_data_10std <- c(
  system.file("extdata", "example_MAGPIX_pk_10std_plate1.csv", package = "SeroTrackR"),
  system.file("extdata", "example_MAGPIX_pk_10std_plate2.csv", package = "SeroTrackR")
)
your_plate_layout_10std <- system.file("extdata", "example_platelayout_pk_10std.xlsx", package = "SeroTrackR")

## -----------------------------------------------------------------------------
results_10stdcurve <- runPlasmoPipeline(
  raw_data = your_raw_data_10std,
  platform = "magpix",
  plate_layout = your_plate_layout_10std,
  panel = "panel1",
  std_point = 10, ################################### here make sure you write 10! 
  experiment_name = "10-point standard curve"
)

## -----------------------------------------------------------------------------
results_10stdcurve$std_curve

## -----------------------------------------------------------------------------
results_10stdcurve$bead_counts

## -----------------------------------------------------------------------------
results_10stdcurve$blanks

## -----------------------------------------------------------------------------
results_10stdcurve$mfi_outputs$All_Results %>%
  head() %>% 
  kable()

## -----------------------------------------------------------------------------
results_10stdcurve$mfi_outputs$MFI_RAU %>%
  head() %>% 
  kable()

## -----------------------------------------------------------------------------
results_10stdcurve$mfi_outputs$MFI_RAU_long %>%
  head() %>% 
  kable()