plot_dataset: Generate an IDOC plot

In shaliulab/idocr: Analyze traces created in the Individual Drosophila Optogenetics Conditioner (IDOC)

Generate an IDOC plot

Description

Take a dataset and its analysis, together with plotting parameters, to visualize an IDOC experiment

Usage

plot_dataset(
  experiment_folder,
  dataset,
  analysis,
  result_folder = NULL,
  plot_preference_index = TRUE,
  plot_decision_zone = TRUE,
  plot_crosses = TRUE,
  subtitle = "",
  colors = c(TREATMENT_A = "red", TREATMENT_B = "blue"),
  labels = c(TREATMENT_A = "TREATMENT_A", TREATMENT_B = "TREATMENT_B"),
  analysis_mask = NULL,
  plot_mask = NULL,
  downward = TRUE,
  nrow = 1,
  ncol = 20,
  suffix = "",
  cross_size = 2,
  line_alpha = 1,
  marker_shape = 16,
  marker_colors = c("#35b347", "#00abee"),
  do_mark_analysis_mask = TRUE,
  do_document = TRUE,
  orientation = "y",
  style = "default",
  ...
)

Arguments

experiment_folder	Path to folder containing IDOC results .csv files
dataset	List of raw data including: roi: every row records the position of one animal at one point in time controller: every row records the status of all IDOC stimulus at one point in time limits border
analysis	List of processed data including: annotation: every row is a decision zone exit and its appetitive / aversive value pi: preference index scored by each animal
result_folder	Path to a folder where to save results. If not passaed, it is set to experiment_folder
plot_preference_index	Whether to show the scored preference index with the region id on the facet label (TRUE), or just the region id (FALSE)
plot_decision_zone	Whether to display the decision zone (TRUE) or not.
plot_crosses	Whether to display the decision zone crosses (TRUE) or not.
subtitle	Character to write on the plot subtitles
colors	Named vector of colors. Values should be colors and names need to map to controller events
labels	Character vector whose values become the name of the treatments as rendered in the plot's legend
analysis_mask	Numeric vector of length 2 containing start and end timepoint of mask in seconds since the start of the experiment Every behavior outside of the mask is ignored
plot_mask	If not NULL, the plot contains data contained within the interval's start and end (s)
downward	Whether the 0 should be at the top (TRUE) or the bottom (FALSE) of the plot
nrow	Number of rows used for facetting data
ncol	Number of cols used for facetting data
suffix	A character (word) that will differentiate resulting output from other output produced on the same experiment folder. Useful for segmenting the experiment into different periods of interest and analyzing these periods separately.
cross_size	Size of dots used to represent decision zone exits (crosses)
line_alpha	Alpha of position trace
...	Extra arguments for save_plot

Details

A corssing dataset where every record represents a decision zone exit of one animal is required to show the exits in the plot

Value

ggplot2 object

See Also

mark_stimuli()

mark_decision_zone()

mark_crosses()

save_plot()

shaliulab/idocr documentation built on June 1, 2025, 4:59 p.m.