Learn R Programming

ddpcr: Analysis and visualization of Droplet Digital PCR data in R and on the web

Created by Dean Attali

This package provides an interface to explore, analyze, and visualize droplet digital PCR (ddPCR) data in R. It also includes an interactive web application with a visual user interface to facilitate analysis for anyone who is not comfortable with using R. The app is available online or it can be run locally.

This document explains the purpose of this package and includes a tutorial on how to use it. It should take about 20 minutes to go through the entire document. A peer-reviewed publication describing this tool is available in F1000Research.

Table of contents

This package is designed to analyze two-channel ddPCR experiments (experiments utilizing both fluorescence channels). Single-channel experiments (where only one fluorescence channel is used) cannot use this tool.

A two-channel assay typically uses one FAM dye and one HEX dye, and consequently the droplets will be grouped into one of four clusters: double-positive (droplets that contain both target sequences and emit both HEX and FAM fluorescence), FAM-positive, HEX-positive, and double-negative (empty droplets without any amplifiable template that do not emit fluorescence in either channel). When plotting the droplets, each quadrant of the plot corresponds to a cluster; for example, the droplets in the lower-left quadrant are the double-negative droplets.

After running a ddPCR experiment, a key step in the analysis is gating the droplets to determine how many droplets belong to each cluster. Bio-Rad provides an analysis software called QuantaSoft which can be used to perform gating. QuantaSoft can either do the gating automatically or allow the user to set the gates manually. Most ddPCR users currently gate their data manually because QuantaSoft’s automatic gating often does a poor job and there are no other tools available for gating ddPCR data.

  • Identify failed wells - identify wells with a failed ddPCR reaction. These wells will be excluded from all downstream analysis. No template control (NTC) wells will be deemed as failures by this tool.
  • Identify outlier droplets - sometimes a few droplets can have an extremely high fluorescent intensity value that is probably erroneous, perhaps as a result of an error with the fluorescence reader. These droplets are identified and removed from the downstream analysis.
  • Identify empty droplets - droplets with very low fluorescent amplitudes are considered empty and are removed from the downstream analysis. Removing these droplets is beneficial for two reasons: 1. the size of the data is greatly reduced, which means the computations will be faster on the remaining droplets, and 2. the real signal of interest is in the non-empty droplets, and empty droplets can be regarded as noise.
  • Calculating template concentration - by knowing how many empty droplets are in each well, the starting concentration of the target DNA in the sample can be calculated (as number of copies of target template per microlitre of sample). Calculate the starting concentration of the target DNA molecule in the sample, defined as the number of copies per microlitre of input.
  • Gating droplets - if your experiment matches some criteria (more on that soon), then automatic gating can take place; otherwise, you can gate the data with custom thresholds just like on QuantaSoft.
  • Explore results - the results from each well (# of drops, # of outliers, # of empty drops, concentration, etc.) can be explored as a histogram or boxplot to see the distribution of all wells in the plate.
  • Plot - you can plot the data in the plate with many customizable parameters
  • The experiment uses a two-channel ddPCR assay with three expected droplet clusters: double-negative, double-positive, and single-positive.
  • The majority of droplets are empty (double-negative).
  • The majority of non-empty droplets are double-positive.
  • There can be a third cluster of either FAM+ or HEX+ droplets, but not both.

In other words, the built-in automatic gating will work when there are three expected clusters of droplets: (1) double-negative, (2) double-positive, and (3) either FAM+ or HEX+. These types of experiments will be referred to as (FAM+)/(FAM+HEX+) or (HEX+)/(FAM+HEX+). Both of these experiment types fall under the name of PNPP experiments; PNPP is short for PositiveNegative/PositivePositive, which is a reflection of the droplet clusters. Here is what a typical well from a PNPP experiment looks like:

If your experiment matches the criteria for a PNPP experiment (either a (FAM+)/(FAM+HEX+) or a (HEX+)/(FAM+HEX+) experiment), then each droplet will be classified either as a rain droplet or as one of the three expected droplet clusters (FAM+, FAM+HEX+, or double-negative). Rain droplets are droplets that emit considerably more fluorescence than empty droplets, but do not emit enough fluorescence to be assigned into one of the main clusters. Here is the result of analyzing a single well from a (FAM+)/(FAM+HEX+) experiment:

If your ddPCR experiment is not a PNPP type, you can still use this tool for the rest of the analysis, exploration, and plotting, but it will not benefit from the automatic gating. However, ddpcr is built to be easily extensible, which means that you can add your own experiment type. Custom experiment types need to define their own method for gating the droplets in a well, and then they can be used in the same way as the built-in experiment types.

Note: throughout this document, FAM will be synonymous to Y axis and HEX will be synonymous to X axis, as a reflection of the fact that conventionally when visualizing the data the FAM intensity is plotted on the Y axis and the HEX intensity is on the X axis.

First, install ddpcr

install.packages("ddpcr")

Note how ddpcr is designed to play nicely with the magrittr pipe %>% for easier pipeline workflows.

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()

#> Warning: package 'bindrcpp' was built under R version 3.4.4

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")

  • 50 data files (well files): each well will have its own file with the name ending in *_Amplitude.csv. For example, the droplets in well A01 will be saved in 2015-05-20_mouse_A01_Amplitude.csv (click on the Export Amplitude and Cluster Data button in the Setup tab).
  • 1 results file: a small file named 2015-05-20_mouse.csv will be generated with some information about the plate, including the name of the sample in each well (click on the Export CSV button in the Analyze tab).

The well files are the only required input to ddpcr, and since ddPCR plates contain 96 wells, you can upload anywhere from 1 to 96 well files. The results file is not mandatory, but if you don’t provide it then the wells will not have sample names attached to them.

ddpcr contains a sample dataset called small that has 5 wells. We use the new_plate() function to initialize a new ddPCR plate object. If given a directory, it will automatically find all the valid well files in the directory and attempt to find a matching results file.

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

#> Reading data files into plate... DONE (0 seconds)
#> Initializing plate of type `ddpcr_plate`... DONE (0 seconds)

You will see some messages appear - every time ddpcr runs an analysis step (initializing the plate is part of the analysis), it will output a message describing what it’s doing. You can turn off messages by disabling the verbose option with the command options(ddpcr.verbose = FALSE).

plot(plate)

Another way to get a quick overview of the data is by simply printing the plate object.

plate

#>                     ddpcr plate
#>                    -------------
#>             Dataset name : small
#>             Data summary : 5 wells; 72,727 drops
#>               Plate type : ddpcr_plate
#> Completed analysis steps : INITIALIZE
#> Remaining analysis steps : REMOVE_FAILURES, REMOVE_OUTLIERS, REMOVE_EMPTY

Among other things, this tells us how many wells and total droplets we have in the data, and what steps of the analysis are remaining. All the information that gets shown when you print a ddpcr plate object is also available through other functions that are dedicated to show one piece of information. For example

plate %>% name()  # equivalent to `name(plate)`

#> [1] "small"

plate %>% type()  # equivalent to `type(plate)`

#> [1] "ddpcr_plate"

Since we didn’t specify an experiment type, this plate object has the default type of ddpcr_plate.

We can see what wells are in our data with wells_used()

plate %>% wells_used()

#> [1] "A01" "A05" "C01" "C05" "F05"

There are 5 wells because the sample data folder has 5 well files.

We can see all the droplets data with plate_data()

plate %>% plate_data()

#> # A tibble: 72,727 x 4
#>    well    HEX   FAM cluster
#>    <chr> <int> <int>   <int>
#>  1 A01     577   494       1
#>  2 A01     515   495       1
#>  3 A01     690   645       1
#>  4 A01     929   860       1
#>  5 A01     844   868       1
#>  6 A01     942   907       1
#>  7 A01     985   923       1
#>  8 A01    1058   966       1
#>  9 A01    1058   979       1
#> 10 A01    1095  1002       1
#> # ... with 72,717 more rows

Technical note: This shows us the fluorescence amplitudes of each droplet, along with the current cluster assignment of each droplet. Right now all droplets are assigned to cluster 1 which corresponds to undefined since no analysis has taken place yet. You can see all the clusters that a droplet can belong to with the clusters() function

plate %>% clusters()
#> [1] "UNDEFINED" "FAILED"    "OUTLIER"   "EMPTY"

This tells us that any droplet in a ddpcr_plate-type experiment can be classified into those clusters. Any droplet is initially UNDEFINED, droplets in failed wells are marked as FAILED, and the other two names are self-explanatory.

We can see the results of the plate so far with plate_meta()

plate %>% plate_meta(only_used = TRUE)

#>   well sample row col used    target_ch1     target_ch2 drops
#> 1  A01   Dean   A   1 TRUE Consensus_FAM WTspecific_HEX 15820
#> 2  A05   Dave   A   5 TRUE Consensus_FAM WTspecific_HEX 13165
#> 3  C01   Mike   C   1 TRUE Consensus_FAM WTspecific_HEX 14256
#> 4  C05  Emily   C   5 TRUE Consensus_FAM WTspecific_HEX 14109
#> 5  F05   Mary   F   5 TRUE Consensus_FAM WTspecific_HEX 15377

The only_used parameter is used so that we’ll only get data about the 5 existing wells and ignore the other 91 unused wells on the plate. Notice that meta (short for metadata) is used instead of results. This is because the meta/results table contains information for each well such as its name, number of drops, number of empty drops, concentration, and many other calculated values.

The subset() function accepts either a list of sample names, a list of wells, or a special range notation. The range notation is a convenient way to select many wells: use a colon (:) to specify a range of wells and a comma (,) to add another well or range. A range of wells is defined as all wells in the rectangular area between the two endpoints. For example, B05:C06 corresponds to the four wells B05, B06, C05, C06. The following diagram shows the result of subsetting with a range notation of A01:H03, C05, E06, B07:C08 on a plate that initially contains all 96 wells.

Back to our data: we have 5 wells, let’s keep 4 of them

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

#> [1] "A01" "A05" "C01" "C05"
plate

#>                     ddpcr plate
#>                    -------------
#>             Dataset name : small
#>             Data summary : 4 wells; 57,350 drops
#>               Plate type : ddpcr_plate
#> Completed analysis steps : INITIALIZE
#> Remaining analysis steps : REMOVE_FAILURES, REMOVE_OUTLIERS, REMOVE_EMPTY

The last two lines show which steps have been completed and which steps remain. These steps are the default steps that any ddpcr plate will go through by default if no type is specified. At this point all we did was load the data, so the initialization step was done and there are 3 remaining steps. You can run all remaining steps with analyze(), or run through the steps one by one using next_step().

plate <- plate %>% analyze()

#> Identifying failed wells... DONE (0 seconds)
#> Identifying outlier droplets... DONE (0 seconds)
#> Identifying empty droplets... DONE (1 seconds)
#> Analysis complete

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

As each step of the analysis is performed, a message describing the current step is printed to the screen. Since we only have 4 wells, it should be very fast, but when you have a full 96-well plate, the analysis could take several minutes. Sometimes it can be useful to run each step individually rather than all of them together if you want to inspect the data after each step.

plate

#>         ddpcr plate
#>        -------------
#> Dataset name : small
#> Data summary : 4 wells; 57,350 drops
#>   Plate type : ddpcr_plate
#>       Status : Analysis completed

We now get a message that says the analysis is complete (earlier it said which steps were remaining). We can also look at the droplets data

plate %>% plate_data()

#> # A tibble: 57,350 x 4
#>    well    HEX   FAM cluster
#>    <chr> <int> <int>   <int>
#>  1 A01     577   494       4
#>  2 A01     515   495       4
#>  3 A01     690   645       4
#>  4 A01     929   860       4
#>  5 A01     844   868       4
#>  6 A01     942   907       4
#>  7 A01     985   923       4
#>  8 A01    1058   966       4
#>  9 A01    1058   979       4
#> 10 A01    1095  1002       4
#> # ... with 57,340 more rows

This isn’t very informative since it shows the cluster assignment for each droplet, which is not easy for a human to digest. Instead, this information can be visualized by plotting the plate (coming up). We can also look at the plate results

plate %>% plate_meta(only_used = TRUE)

#>   well sample row col used    target_ch1     target_ch2 drops success
#> 1  A01   Dean   A   1 TRUE Consensus_FAM WTspecific_HEX 15820    TRUE
#> 2  A05   Dave   A   5 TRUE Consensus_FAM WTspecific_HEX 13165    TRUE
#> 3  C01   Mike   C   1 TRUE Consensus_FAM WTspecific_HEX 14256    TRUE
#> 4  C05  Emily   C   5 TRUE Consensus_FAM WTspecific_HEX 14109   FALSE
#>   drops_outlier drops_empty drops_non_empty drops_empty_fraction
#> 1             2       13690            2130                0.865
#> 2             1       11283            1882                0.857
#> 3             0       12879            1377                0.903
#> 4             0          NA              NA                   NA
#>   concentration
#> 1           170
#> 2           181
#> 3           120
#> 4            NA

Now there’s a bit more information in the results table. The success column indicates whether or not the ddPCR run was successful in that particular well; notice how well C05 was deemed a failure, and thus is not included the any subsequent analysis steps.

You can use the well_info() function to get the value of a specific variable of a specific well from the results. For example, we can query the plate object to see how many empty droplets are in well A05.

well_info(plate, "A05", "drops_empty")

#> [1] 11283
plate %>% plot()

Notice well C05 is grayed out, which means that it is a failed well. By default, failed wells have a grey background, and empty and outlier droplets are excluded from the plot.

You don’t have to analyze a plate object before you can plot it - a ddPCR plate can be plotted at any time to show the data in it. If you plot a plate before analyzing it, it’ll show the raw data.

The following two plots show examples of how to use some plot parameters.

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")

To see all the available plot parameters, run ?plot.ddpcr_plate.

You can also save a ddPCR plate object using plate_save(). This will create a single .rds file that contains an exact copy of the plate’s current state, including all the data, attributes, and analysis progress of the plate. The resulting file can be loaded to restore the ddPCR object at a later time with plate_load().

plate %>% save_plate("myplate")
from_file <- load_plate("myplate")
identical(plate, from_file)

#> [1] TRUE

unlink("myplate.rds")
  1. plate_types$custom_thresholds - when you want to gate your droplets into four quadrants according to HEX and FAM values that you set
  2. plate_types$fam_positive_pnpp - when you have a FAM-positive PNPP plate (FAM+)/(FAM+HEX+)
  3. plate_types$hex_positive_pnpp - when you have a HEX-positive PNPP plate (HEX+)/(FAM+HEX+)

The next two sections explain how to use these experiment types.

# 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)

#> [1] TRUE

plate_manual

#>                     ddpcr plate
#>                    -------------
#>             Dataset name : small
#>             Data summary : 4 wells; 57,350 drops
#>               Plate type : custom_thresholds, ddpcr_plate
#> Completed analysis steps : INITIALIZE
#> Remaining analysis steps : REMOVE_OUTLIERS, CLASSIFY

It’s usually a good idea to take a look at the raw data to decide where the draw the thresholds

plot(plate_manual, show_grid_labels = TRUE)

If you noticed, there’s a droplet in well A05 that has a much larger fluorescence value and is probably an outlier, which is the reason the scale is a bit too large. After analyzing the plate, it will be identified as an outlier and hidden automatically. Before running the analysis, we should set where the thresholds will be. By default, the thresholds are at (5000, 5000), which is very arbitrary. It looks like the x coordinate is fine, but the y border should move up to approximately 8000. Then run the analysis.

# what are the current thresholds?
thresholds(plate_manual)

#> [1] "(5000, 5000)"

# set the thresholds to (5000,8000)
thresholds(plate_manual) <- c(5000, 8000)
plate_manual <- analyze(plate_manual)

#> Identifying outlier droplets... DONE (0 seconds)
#> Classifying droplets... DONE (0 seconds)
#> Analysis complete

Now the plate is ready and we can plot it or look at its results

plate_meta(plate_manual, only_used = TRUE)

#>   well sample row col used    target_ch1     target_ch2 drops
#> 1  A01   Dean   A   1 TRUE Consensus_FAM WTspecific_HEX 15820
#> 2  A05   Dave   A   5 TRUE Consensus_FAM WTspecific_HEX 13165
#> 3  C01   Mike   C   1 TRUE Consensus_FAM WTspecific_HEX 14256
#> 4  C05  Emily   C   5 TRUE Consensus_FAM WTspecific_HEX 14109
#>   drops_outlier drops_empty drops_x_positive drops_y_positive
#> 1             2       13909               20               20
#> 2             1       11512               34              390
#> 3             0       12967                8                7
#> 4             0       14011               15               11
#>   drops_both_positive
#> 1                1869
#> 2                1228
#> 3                1274
#> 4                  72

plot(plate_manual)

By default, the droplets in each quadrant are a different colour. If you want to change the colour of some droplets, we can use the col_drops_* parameter as before. Since now we’re working with a different plate type, the names of the droplet clusters can be different, so we need to first know what they are

clusters(plate_manual)

#> [1] "UNDEFINED"     "OUTLIER"       "EMPTY"         "X_POSITIVE"   
#> [5] "Y_POSITIVE"    "BOTH_POSITIVE"

Now if we want to change the colour of the double-positive droplets to red, we just add a parameter col_drops_both_positive = "red".

To see all the available plot parameters for this plate type, run ?plot.custom_thresholds. In addition, any plot parameter that is available for default plates can also be used here (all parameters listed under ?plot.ddpcr_plate).

Let’s create a new plate object of the desired type.

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

#> Reading data files into plate... DONE (0 seconds)
#> Initializing plate of type `fam_positive_pnpp`... DONE (0 seconds)

If the data were (HEX+)/(FAM+HEX+), we would have used type = plate_types$hex_positive_pnpp instead.

clusters(plate_pnpp)

#> [1] "UNDEFINED" "FAILED"    "OUTLIER"   "EMPTY"     "RAIN"      "POSITIVE" 
#> [7] "NEGATIVE"

The first 4 clusters we’ve seen before, as they are common to all plate types. Droplets in the HEX+FAM+ cluster are considered POSITIVE, while droplets in the FAM+ cluster are considered NEGATIVE since they are HEX-. Any droplets that are not empty but don’t emit enough fluorescent intensity to be in the POSITIVE or NEGATIVE clusters are considered RAIN.

When using the plate_types$fam_positive_pnpp type, the positive droplets (FAM+HEX+) are called wildtype, and the negative droplets (FAM+HEX-) are called mutant. Why? This package was originally designed to analyze a specific assay where the FAM+HEX+ cluster represented droplets with a wildtype gene inside, while the FAM+HEX- cluster corresponded to droplets with a mutant gene. Talking about positive vs negative drops or positive vs negative wells sounds a bit weird, so it was decided to stick with mutant vs wildtype. Just remember: wildtype = double-positive droplets, mutant = singly-positive droplets.

plate_pnpp <- analyze(plate_pnpp)

#> Identifying failed wells... DONE (0 seconds)
#> Identifying outlier droplets... DONE (0 seconds)
#> Identifying empty droplets... DONE (0 seconds)
#> Classifying droplets... DONE (0 seconds)
#> Reclassifying droplets... skipped (not enough wells with significant mutant clusters)
#> Analysis complete

One of the key goals in running the analysis is to determine the number of POSITIVE (wildtype) and NEGATIVE (mutant) droplets in each well, and similarly the mutant frequency (if a well has 95 wildtype droplets and 5 mutant droplets, then the mutant frequency in the well is 5%).

You can see from the output that the two last steps are classifying and reclassifying the droplets, and that the reclassification didn’t take place. The classification step identifies all the non-empty droplets as either rain, mutant, or wildtype by analyzing each well individually. Wells with a very low mutant frequency (i.e. there are very few mutant droplets) are much harder to gate accurately, which is the reason for the reclassification step. The reclassification step uses information from wells with high a mutant frequency, where the gates are more clearly defined, to adjust the gates in wells with a low mutant frequency. The reclassification step only takes place if there are enough wells with a high mutant frequency.

plate_pnpp %>% plate_meta(only_used = TRUE)

#>   well sample row col used    target_ch1     target_ch2 drops success
#> 1  A01   Dean   A   1 TRUE Consensus_FAM WTspecific_HEX 15820    TRUE
#> 2  A05   Dave   A   5 TRUE Consensus_FAM WTspecific_HEX 13165    TRUE
#> 3  C01   Mike   C   1 TRUE Consensus_FAM WTspecific_HEX 14256    TRUE
#> 4  F05   Mary   F   5 TRUE Consensus_FAM WTspecific_HEX 15377    TRUE
#> 5  C05  Emily   C   5 TRUE Consensus_FAM WTspecific_HEX 14109   FALSE
#>   drops_outlier drops_empty drops_non_empty drops_empty_fraction
#> 1             2       13690            2130                0.865
#> 2             1       11283            1882                0.857
#> 3             0       12879            1377                0.903
#> 4             0       14126            1251                0.919
#> 5             0          NA              NA                   NA
#>   concentration mutant_border filled_border significant_mutant_cluster
#> 1           170          4194          8286                      FALSE
#> 2           181          3789          8136                       TRUE
#> 3           120          4356          8445                      FALSE
#> 4            99          3926          8294                       TRUE
#> 5            NA            NA            NA                         NA
#>   mutant_num wildtype_num mutant_freq
#> 1          4         1827       0.218
#> 2        368         1224      23.100
#> 3          3         1248       0.240
#> 4        211          855      19.800
#> 5         NA           NA          NA

Explanation of some of the variables:

  • mutant_num and wildtype_num - the number of mutant and wildtype droplets
  • mutant_freq - the frequency (0-1) of non-empty, non-rain droplets that are in the mutant cluster
  • significant_mutant_cluster - TRUE if the the well contains a statistically significant number of mutant droplets

Plotting the data is usually the best way to see the results

plate_pnpp %>% plot(text_size_mutant_freq = 8)

To see all the available plot parameters for this plate type, run ?plot.pnpp_experiment. In addition, any plot parameter that is available for default plates can also be used here (all parameters listed under ?plot.ddpcr_plate).

The wildtype droplets are green and the mutant droplets are purple. The well colours themselves reflect the significant_mutant_cluster variable: wells that are mostly wildtype droplets are green, and wells with significant mutant clusters are purple. There are parameters to set all these colours, the transparency levels, and many more options.

Similar to how wells_failed() returns the failed wells, you can use the wells_mutant() and wells_wildtype() functions to extract the wells with a significant mutant cluster and those without.

plate_pnpp %>% wells_mutant()

#> [1] "A05" "F05"

plate_pnpp %>% wells_wildtype()

#> [1] "A01" "C01"
plate %>% params() %>% str()

#> List of 4
#>  $ GENERAL        :List of 4
#>   ..$ X_VAR         : chr "HEX"
#>   ..$ Y_VAR         : chr "FAM"
#>   ..$ DROPLET_VOLUME: num 0.00085
#>   ..$ RANDOM_SEED   : num 8
#>  $ REMOVE_FAILURES:List of 3
#>   ..$ TOTAL_DROPS_T      : num 5000
#>   ..$ EMPTY_LAMBDA_LOW_T : num 0.3
#>   ..$ EMPTY_LAMBDA_HIGH_T: num 0.99
#>  $ REMOVE_OUTLIERS:List of 2
#>   ..$ TOP_PERCENT: num 1
#>   ..$ CUTOFF_IQR : num 5
#>  $ REMOVE_EMPTY   :List of 1
#>   ..$ CUTOFF_SD: num 7

You can also view the parameters for a specific step or the value of a parameter. For example, to see the parameters used in the step that identifies failed wells, use

plate %>% params("REMOVE_FAILURES")

#> $TOTAL_DROPS_T
#> [1] 5000
#> 
#> $EMPTY_LAMBDA_LOW_T
#> [1] 0.3
#> 
#> $EMPTY_LAMBDA_HIGH_T
#> [1] 0.99

You can also view or edit specific parameters. When identifying failed wells, one of the conditions for a successful run is to have at least 5,000 droplets in the well (Bio-Rad claims that every well has 20,000 droplets). If you know that your particular experiment had much fewer droplets than usual and as a result ddpcr thinks that all the wells are failures, you can change the setting

params(plate, "REMOVE_FAILURES", "TOTAL_DROPS_T")

#> [1] 5000

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

#> [1] 1000

If you look at the full parameters of the plate, you’ll notice that by default ddpcr assumes that the dyes used are FAM and HEX. If you are using a different dye and want the name of that dye appear in the results instead, you can use the x_var() or y_var() functions.

orig_x <- x_var(plate)
orig_x

#> [1] "HEX"

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

#> [1] "well"    "VIC"     "FAM"     "cluster"

x_var(plate) <- orig_x

Note that if you change any parameters, you need to re-run the analysis. If you try running analyze() after a plate has already been analyzed, you will simply get a message saying the plate is already analyzed. To force an already-analyzed plate to re-run the analysis, you need to use the restart = TRUE parameter.

plate <- analyze(plate)

#> Analysis complete

plate <- analyze(plate, restart = TRUE)

#> Restarting analysis

#> Initializing plate of type `ddpcr_plate`... DONE (0 seconds)
#> Identifying failed wells... DONE (0 seconds)
#> Identifying outlier droplets... DONE (0 seconds)
#> Identifying empty droplets... DONE (1 seconds)
#> Analysis complete
plate_pnpp %>% steps

#> $INITIALIZE
#> [1] "init_plate"
#> 
#> $REMOVE_FAILURES
#> [1] "remove_failures"
#> 
#> $REMOVE_OUTLIERS
#> [1] "remove_outliers"
#> 
#> $REMOVE_EMPTY
#> [1] "remove_empty"
#> 
#> $CLASSIFY
#> [1] "classify_droplets"
#> 
#> $RECLASSIFY
#> [1] "reclassify_droplets"

This list contains all the steps of analyzing the given plate, with each item in the list containing both the name of the step and the R function that performs it. For example, the first step is INITIALIZE and it uses the function init_plate(). You can see the code for that function by running ddpcr:::init_plate.

ddpcr:::init_plate

#> function(plate) {
#>   stopifnot(plate %>% inherits("ddpcr_plate"))
#>   step_begin(sprintf("Initializing plate of type `%s`", type(plate)))
#> 
#>   plate %<>%
#>     set_default_clusters %>%
#>     set_default_steps %>%
#>     init_data %>%
#>     init_meta
#> 
#>   status(plate) <- step(plate, 'INITIALIZE')
#>   plate[['version']] <- as.character(utils::packageVersion("ddpcr"))
#>   plate[['dirty']] <- FALSE
#>   step_end()
#> 
#>   plate
#> }
#> <environment: namespace:ddpcr>

For more details about the algorithm, see the Algorithms vignette.

For more details about how to create new plate types, see the Extending ddpcr by adding new plate types vignette.

For details on the technical details regarding the code implementation, see the Technical details vignette.

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Install

install.packages('ddpcr')

Monthly Downloads

544

Version

1.15.2

License

MIT + file LICENSE

Issues

0

Pull Requests

0

Stars

60

Forks

33

Maintainer

Dean Attali

Last Published

August 20th, 2023

Functions in ddpcr (1.15.2)

col_to_num

Convert a plate column to a number
custom_thresholds

Plate type: custom thresholds
get_empty_cutoff.ddpcr_plate

Get the cutoff for empty droplets in a well
get_outlier_cutoff.ddpcr_plate

Get the cutoff for outliers
define_clusters.custom_thresholds

Define droplet clusters for custom thresholds plates
define_clusters

Define droplet clusters
define_params.ddpcr_plate

Define plate type parameters for default plates
fam_positive_pnpp

Plate type: FAM-positive PNPP
get_outlier_cutoff

Get the cutoff for outliers
get_col

Get column from well ID
err_msg

Show an error message
define_params.fam_positive_pnpp

Define plate type parameters for FAM-positive PNPP
cluster

Get cluster ID by name
define_params.pnpp_experiment

Define plate type parameters for PNPP experiments
diff.point2d

Euclidean distance between two points
get_wells_btwn

Get all wells between two wells (assume a rectangle layout)
classify_thresholds

Analysis step: Classify droplets
define_steps.pnpp_experiment

Define analysis steps for PNPP experiments
%>%

magrittr forward-pipe operator
is_range

Is the given parameter a range?
get_single_well

Get droplet data from a well
define_params.hex_positive_pnpp

Define plate type parameters for HEX-positive PNPP
get_empty_cutoff.pnpp_experiment

Get the cutoff for empty droplets in a well
%btwn%

Determine if a numeric value is within a range
get_row

Get row from well ID
get_empty_cutoff

Get the cutoff for empty droplets in a well
cluster_name

Get cluster name by ID
is_well_success.ddpcr_plate

Determine if a well had a successful ddPCR run
clusters

Potential droplet clusters for a plate type
is_empty_plate

Is a plate empty?
has_signif_negative_cluster

Does a well have a statistically significant number of negative droplets?
is_well_success

Determine if a well had a successful ddPCR run
parent_plate_type

Parent plate type
mark_clusters

Mark the clusters of droplets only in certain wells to their assigned cluster
parent_plate_type.default

Parent plate type of any plate
plate_data<-

Overwrite the plate data
parent_plate_type.fam_positive_pnpp

Parent plate type of FAM-positive PNPP
lol_to_df

Convert a list of lists returned from vapply to a dataframe
hex_positive_pnpp

Plate type: HEX-positive PNPP
load_plate

Load a previously saved ddPCR plate
launch

Run the interactive analysis tool (Shiny app) in a web browser
define_steps.custom_thresholds

Define analysis steps for custom thresholds plates
parent_plate_type.hex_positive_pnpp

Parent plate type of HEX-positive PNPP
parent_plate_type.ddpcr_plate

Parent plate type of default plates
is_file

Determine if a given path is a valid file
range_list_to_vec

Convert a list of ranges to a vector of its individual components
define_params

Define plate type parameters
has_step

Does a ddPCR plate have a step with this name?
is_well_success.pnpp_experiment

Determine if a well had a successful ddPCR run
define_steps.ddpcr_plate

Define analysis steps for default plates
define_clusters.ddpcr_plate

Define droplet clusters for default plates
define_params.custom_thresholds

Define plate type parameters for custom thresholds plates
msg

Write a message to the user if the `ddpcr.verbose` option is on
define_clusters.pnpp_experiment

Define droplet clusters for PNPP experiments
parent_plate_type.wildtype_mutant_pnpp

Parent plate type of wildtype/mutant PNPP
plate_data

Plate data (droplets data)
plot.ddpcr_plate

Plot a ddPCR plate
name

Plate name
define_params.wildtype_mutant_pnpp

Define plate type parameters for wildtype/mutant PNPP
move_back

Move columns to the back of a data.frame
other_dim

Given an axis (X or Y), return the other
positive_dim_var

Name of dye in positive dimension in PNPP experiment
positive_name

Name identifier for positive and negative droplets
remove_failures

Analysis step: Remove failed wells
move_front

Move columns to the front of a data.frame
positive_dim

Positive dimension in a PNPP experiment
define_steps

Define analysis steps
plot.pnpp_experiment

Plot a ddPCR plate of type PNPP experiment
point2d

Representation of a 2D point
get_filled_border

Get border of filled droplets in PNPP experiment
plot.wildtype_mutant_pnpp

Plot a ddPCR plate of type wildtype/mutant PNPP
merge_dfs_overwrite_col

Overwrite a column in a data.frame based on a matching column in another df
num_to_col

Convert a number to plate column
meta_var_name

Name of variable in PNPP experiment metadata
plate_meta

Plate metadata
params

Plate parameters
num_to_row

Convert a number to plate row
plate_meta<-

Overwrite the plate metadata
reset

Reset a plate
pnpp_experiment

Plate type: PNPP experiment
remove_empty.ddpcr_plate

Analysis step: Remove empty droplets
row_to_num

Convert a plate row to a number
remove_empty.pnpp_experiment

Analysis step: Remove empty droplets
reclassify_droplets.pnpp_experiment

Analysis step: Reclassify droplets
remove_outliers.ddpcr_plate

Analysis Step: Remove outlier droplets
reclassify_droplets_single

Reclassify droplets in a well
get_filled_drops

Get filled droplets in PNPP experiment
save_plate

Save a ddPCR plate
remove_outliers

Analysis Step: Remove outlier droplets
is_dirty

Is the plate object dirty (ie has changed since the analysis was run)?
remove_failures.ddpcr_plate

Analysis step: Remove failed wells
steps

Analysis steps of a ddPCR plate
is_dir

Determine if a given path is a valid directory
sample_data

Get sample data
y_threshold

Get/set the Y threshold
range_to_seq

Convert a range to a vector of all elements between the endpoints
step_end

Inform the user that an analysis step finished
range_to_endpoints

Extract the two endpoints of a range
step_name

Get step name by ID
set_default_params

Reset plate parameters to their defaults
warn_msg

Show a warning message
variable_dim_var

Name of dye in variable dimension in PNPP experiment
reclassify_droplets

Analysis step: Reclassify droplets
subset.ddpcr_plate

Subsetting a ddPCR plate
wells_used

Get wells used in a ddPCR plate
wells_success

Get successful/failed wells
local_maxima

Get the indices of the local maxima in a list of numbers
local_minima

Get the indices of the local minima in a list of numbers
type

Plate type
named_vec_to_df

Convert a named vector returned from vapply to a dataframe
thresholds

Get/set the thresholds
new_plate

Create a new ddPCR plate
status

Plate status
x_threshold

Get/set the X threshold
variable_dim

Variable dimension in a PNPP experiment
unanalyzed_clusters

Get unanalyzed cluseter IDs
wells_negative

Get negative wells
x_var

Get/set the X/Y variable (dye name)
normalize_to_rds

Normalize a file name to .rds suffix
quiet

Suppress all output from an expression. Works cross-platform.
step

Get step ID by step name
wells_positive

Get positive wells
print.ddpcr_plate

Print info about a ddPCR plate
remove_empty

Analysis step: Remove empty droplets
next_step

Run the next step in an analysis
wildtype_mutant_pnpp

Plate type: wildtype/mutant PNPP
wells_wildtype

Get wildtype wells
plot.custom_thresholds

Plot a ddPCR plate of type custom thresholds
step_begin

Inform the user that an analysis step is starting
well_info

Get metadata info of a well
reclassify_droplets_single.pnpp_experiment

Reclassify droplets in a well
plate_types

Supported plate types
wells_mutant

Get mutant wells
calc_negative_freq_simple

Calculate negative frequency based on number of drops
analyze

Run analysis on a ddPCR plate
analysis_complete

Is the analysis complete?
capitalize

Capitalize the first letter of a string
WELL_ID_REGEX

regex for a well ID
calculate_neg_freq_single

Calculate negative frequency of a single well
bind_df_ends

Helper function for move_front and move_back
calculate_negative_freqs

Calculate negative frequencies in whole plate
classify_droplets

Analysis step: Classify droplets
classify_droplets.pnpp_experiment

Analysis step: Classify droplets
calculate_concentration

Calculate template concentration
calculate_concentration_single

Calculate concentration in a single well
cat0

Concatenate strings with no space between them
check_step

Ensure the plate's status is at the right step
ddpcr-package

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

Classify droplets in a well
classify_droplets_single.pnpp_experiment

Classify droplets in a well
ddpcr_plate

Plate type: ddPCR plate