inst/doc/overview.R

In ddpcr: Analysis and Visualization of Droplet Digital PCR in R and on the Web

## ----setup, echo = FALSE, message = FALSE-------------------------------------
knitr::opts_chunk$set(tidy = FALSE, comment = "#>")
options(ddpcr.verbose = TRUE)

## ----installpkg, eval = FALSE-------------------------------------------------
#  install.packages("ddpcr")

## ----quickstart, message = FALSE, fig.show='hold', out.width='50%', fig.retina=FALSE----
library(ddpcr)
dir <- sample_data_dir()

# example 1: manually set thresholds
plate1 <-
  new_plate(dir, type = plate_types$custom_thresholds) %>%
  subset("A01,A05") %>%
  set_thresholds(c(5000, 7500)) %>%
  analyze()
plot(plate1, show_grid_labels = TRUE, alpha_drops = 0.3,
       title = "Manually set gating thresholds\nworks with any data")

# example 2: automatic gating
new_plate(dir, type = plate_types$fam_positive_pnpp) %>%
  subset("A01:A05") %>%
  analyze() %>%
  plot(show_mutant_freq = FALSE, show_grid_labels = TRUE, alpha_drops = 0.3,
       title = "Automatic gating\nworks with PNPP experiments")

## ----readdata-----------------------------------------------------------------
library(ddpcr)
dir <- sample_data_dir()
plate <- new_plate(dir)

## ----plotraw------------------------------------------------------------------
plot(plate)

## ----printprint---------------------------------------------------------------
plate

## ----explore-1----------------------------------------------------------------
plate %>% name()  # equivalent to `name(plate)`
plate %>% type()  # equivalent to `type(plate)`

## ----explore-2----------------------------------------------------------------
plate %>% wells_used()

## ----explore-3----------------------------------------------------------------
plate %>% plate_data()

## ----explore-5----------------------------------------------------------------
plate %>% plate_meta(only_used = TRUE)

## ----subset-------------------------------------------------------------------
plate <- plate %>% subset("A01:C05")
# could have also used subset("A01, A05, C01, C05")
plate %>% wells_used()

## ----steps--------------------------------------------------------------------
plate

## ----analyze------------------------------------------------------------------
plate <- plate %>% analyze()
# equivalent to `plate %>% next_step(3)`
# also equivalent to `plate %>% next_step() %>% next_step() %>% next_step()`

## ----explore-post-1-----------------------------------------------------------
plate

## ----explore-post-2-----------------------------------------------------------
plate %>% plate_data()

## ----explore-post-3-----------------------------------------------------------
plate %>% plate_meta(only_used = TRUE)

## ----explore-post-4-----------------------------------------------------------
well_info(plate, "A05", "drops_empty")

## ----plotsimple---------------------------------------------------------------
plate %>% plot()

## ----plotparams, fig.show='hold', out.width='50%', fig.retina=FALSE-----------
plate %>% plot(wells = "A01,A05", show_full_plate = TRUE,
               show_drops_empty = TRUE, col_drops_empty = "red",
               title = "Show full plate")
plate %>% plot(wells = "A01,A05", superimpose = TRUE,
               show_grid = TRUE, show_grid_labels = TRUE, title = "Superimpose")

## ----saveload-----------------------------------------------------------------
plate %>% save_plate("myplate")
from_file <- load_plate("myplate")
identical(plate, from_file)
unlink("myplate.rds")

## ----reset, message=FALSE-----------------------------------------------------
# two ways to create the desired plate
plate_manual <- reset(plate, type = plate_types$custom_thresholds)
plate_manual2 <- new_plate(dir, type = plate_types$custom_thresholds) %>%
  subset("A01:C05")

# make sure the two methods above are identical
identical(plate_manual, plate_manual2)

plate_manual

## ----plotcrosshair------------------------------------------------------------
plot(plate_manual, show_grid_labels = TRUE)

## ----setthresholds------------------------------------------------------------
# what are the current thresholds?
thresholds(plate_manual)
# set the thresholds to (5000,8000)
thresholds(plate_manual) <- c(5000, 8000)
plate_manual <- analyze(plate_manual)

## ----crosshairresults---------------------------------------------------------
plate_meta(plate_manual, only_used = TRUE)
plot(plate_manual)

## ----crosshairclusters--------------------------------------------------------
clusters(plate_manual)

## ----pnppdefine---------------------------------------------------------------
plate_pnpp <- new_plate(dir, type = plate_types$fam_positive_pnpp)

## ----pnppclusters-------------------------------------------------------------
clusters(plate_pnpp)

## ----pnppanalyze--------------------------------------------------------------
plate_pnpp <- analyze(plate_pnpp)

## ----pnppmeta-----------------------------------------------------------------
plate_pnpp %>% plate_meta(only_used = TRUE)

## ----pnppplot-----------------------------------------------------------------
plate_pnpp %>% plot(text_size_mutant_freq = 8)

## ----pnppnegpos---------------------------------------------------------------
plate_pnpp %>% wells_mutant()
plate_pnpp %>% wells_wildtype()

## ----paramsstr----------------------------------------------------------------
plate %>% params() %>% str()

## ----paramsfailures-----------------------------------------------------------
plate %>% params("REMOVE_FAILURES")

## ----setparams----------------------------------------------------------------
params(plate, "REMOVE_FAILURES", "TOTAL_DROPS_T")
params(plate, "REMOVE_FAILURES", "TOTAL_DROPS_T") <- 1000
params(plate, "REMOVE_FAILURES", "TOTAL_DROPS_T")

## ----changexvar---------------------------------------------------------------
orig_x <- x_var(plate)
orig_x
x_var(plate) <- "VIC"
plate %>% plate_data() %>% names()
x_var(plate) <- orig_x

## ----reanalyze----------------------------------------------------------------
plate <- analyze(plate)
plate <- analyze(plate, restart = TRUE)

## ----exactsteps---------------------------------------------------------------
plate_pnpp %>% steps

## ----stepsource---------------------------------------------------------------
ddpcr:::init_plate