plot.ddpcr_plate {ddpcr}

Plot a ddPCR plate

Description

Plot the data of a ddPCR plate. A plate can be plotted throughout any stage of the analysis, and the most up-to-date data will be shown. For example, a plot performed after initializing a plat will show all the raw data, but a plot performed after analyzing a plate will show information such as empty drops and failed wells.

Usage

## S3 method for class 'ddpcr_plate'
plot(
  x,
  wells,
  samples,
  superimpose = FALSE,
  show_full_plate = FALSE,
  show_drops = TRUE,
  show_drops_empty = FALSE,
  show_drops_outlier = FALSE,
  show_failed_wells = TRUE,
  col_drops = "black",
  col_drops_undefined = col_drops,
  col_drops_failed = col_drops,
  col_drops_empty = col_drops,
  col_drops_outlier = "orange",
  bg_plot = "transparent",
  bg_failed = "#111111",
  bg_unused = "#FFFFFF",
  alpha_drops = 0.2,
  alpha_drops_outlier = 1,
  alpha_bg_failed = 0.7,
  xlab = x_var(plate),
  ylab = y_var(plate),
  title = NULL,
  show_grid = FALSE,
  show_grid_labels = FALSE,
  drops_size = 1,
  text_size_title = 14,
  text_size_row_col = 12,
  text_size_axes_labels = 12,
  text_size_grid_labels = 12,
  ...
)

Arguments

x

A ddPCR plate.

wells

Only plot selected wells. Supports range notation, see subset.ddpcr_plate.

samples

Only plot selected samples.

superimpose

If TRUE, show all wells superimposed in one plot; otherwise, show wells in a grid.

show_full_plate

If TRUE, show full 96-well plate; otherwise, show only plate rows and columns that are used.

show_drops

Whether or not to show the droplets. Setting to FALSE is not useful if the droplets are the only thing shown in the plot, but it can be useful if there is other information depicated in the plot, such as any background colours or text that may appear in each well.

show_drops_empty

Whether or not to show the droplets defined as empty. See 'Droplet visibility options' below.

show_drops_outlier

Whether or not to show the droplets defined as outliers. See 'Droplet visibility options' below.

show_failed_wells

Whether or not to include wells that are deemed as failed ddPCR runs.

col_drops

The default colour to use for any droplet.

col_drops_undefined

The colour to use for droplets that have not been analyzed yet. See 'Droplet visibility options' below.

col_drops_failed

The colour to use for droplets in failed wells. See 'Droplet visibility options' below.

col_drops_empty

The colour to use for empty droplets. See 'Droplet visibility options' below.

col_drops_outlier

The colour to use for outlier droplets. See 'Droplet visibility options' below.

bg_plot

The background colour for the plot.

bg_failed

The background colour to use for failed wells.

bg_unused

The background colour to use for unused wells.

alpha_drops

The transparency of droplets.

alpha_drops_outlier

The transparency of outlier droplets. See 'Droplet visibility options' below.

alpha_bg_failed

The transparency of the background of failed wells.

xlab

The label on the X axis.

ylab

The label on the Y axis.

title

The title for the plot.

show_grid

Whether or not to show grid lines.

show_grid_labels

Whether or not to show numeric labels for the grid lines along the axes.

drops_size

Size of droplets.

text_size_title

Text size of the title.

text_size_row_col

Text size of the row and column labels.

text_size_axes_labels

Text size of the X/Y axis labels.

text_size_grid_labels

Text size of the numeric grid line labels.

...

Ignored.

Value

A ggplot2 plot object.

Droplet visibility options

To make it easier to support any plate type with any types of droplet clusters, there are three categories of special parameters that can always be used:

• show_drops_* Whether or not to show a specific group of droplets.

• col_drops_* What colour to use for a specific group of droplets.

• alpha_drops_* What transparency to use for a specific group of droplets.

The * in the parameter name can be replaced by the name of any droplet cluster. Use the clusters function to find out what clusters the droplets in a plate can be assigned to.

For example, the default clusters that exist in a plain ddpcr_plate are "UNDEFINED", "FAILED", "OUTLIER", and "EMPTY". This means that if you want to hide the empty drops and make the transparency of drops in failed wells 0.5, you could add the two parameters show_drops_empty = FALSE and alpha_drops_failed = 0.5. Note that letter case is not important. If another plate type defines a new clsuter of type "MUTANT" and you want to show these drops in red, you can add the parameter col_drops_mutant = "red".

Note that some of the more common combinations of these parameters are defined by default (for example, col_drops_failed is defined in the list of parameters), but these three parameter categories will work for any cluster type.

Extending ddpcr_plate

If you create your own plate type, this default plot function might be enough if there is no extra information you want to display in a plot. If you do need to provide a more customized plot function, it can be a good idea to use the output from this plot function as a basis and only add the code that is necessary to append to the plot. See plot.custom_thresholds as an example of how to extend this plot function.

Examples

## Not run: 
plate <- new_plate(sample_data_dir())
plot(plate)
plate <- plate %>% analyze
plot(plate)
plot(plate, "A01:C05", show_drops_empty = TRUE, col_drops_empty = "red")

## End(Not run)