Generate basic QC plots for Tocky data — plot

This function visualizes either Timer fluorescence (Blue vs Red) or Timer dynamics by the Tocky method (Angle vs Intensity) based on the specified mode.

Usage

plot_tocky(
  x,
  file = "PlotTocky",
  pseudocolour = TRUE,
  pdf = FALSE,
  output = "QC",
  n = 4,
  plot_mode = "Timer fluorescence",
  lower_quantile_cutoff = 0.01,
  select = FALSE,
  use_group = TRUE,
  group_order = NULL,
  interactive = TRUE,
  save = FALSE,
  samplefile = NULL,
  verbose = TRUE
)

Arguments

x: A TockyPrepData object returned by `timer_transform`, which sample grouping has been defined by `sample_definition`.
file: File name.
pseudocolour: A logical argument for whether to use pseudocolour in plots.
pdf: A logical argument; if FALSE, a jpeg file is generated instead.
output: The output directory name for output files.
n: A number; n x n plots will be generated in the output Tocky plot file, max is 4 for 16 plots.
plot_mode: Either "Timer fluorescence" for Blue vs Red plots, "Normalized Timer fluorescence" for normalized plots, or "Timer Angle and Intensity" for Angle vs Intensity plots.
lower_quantile_cutoff: Lower quantile cutoff for setting the plot ranges in fluorescence mode.
select: Logical indicating whether to manually select samples for plotting.
use_group: Logical indicating whether to group plots based on the `group` field in `sampledef`.
group_order: Optional character vector for specifying the order of the panels when using the group option.
interactive: Logical indicating whether to prompt the user to select plot_mode. Defaults to `TRUE`.
save: A logical argument; if FALSE, plots are shown in an X window.
samplefile: Character vector specifying the sample files. Defaults to `NULL`.
verbose: Logical indicating whether to print progress messages. Default is `TRUE`.

Examples

if (FALSE) { # \dontrun{
  plot_tocky(x, plot_mode = "Timer fluorescence")
  plot_tocky(x, plot_mode = "Timer Angle and Intensity")
} # }