heatmapGIF: Morris water maze heatmap GIF
In Thonnard/VisualMWM: R functions to visualize Morris water maze data

View source: R/heatmapGIF.R

heatmapGIF

R Documentation

Morris water maze heatmap GIF

Description

The heatmapGIF function creates a raster or contour heatmap GIF of the animal for a specific trial.

Usage

heatmapGIF(
  data,
  id,
  day,
  trial,
  centerx,
  centery,
  radius = 75,
  platformx,
  platformy,
  platformradius = 7.5,
  ndata_circle = 100,
  remove_data_outside_maze = TRUE,
  platform_colour = NA,
  platform_alpha = 1,
  platform_linetype = "solid",
  platform_line_colour = "black",
  platform_line_size = 0.5,
  heatmap_low = "yellow",
  heatmap_high = "red",
  type = "raster",
  interpolate = TRUE,
  contour_filled = TRUE,
  contour_colour_scaled = FALSE,
  contour_colour_filled = NA,
  contour_colour = "blue",
  loop = FALSE,
  width = 480,
  height = 480,
  duration = 10,
  frames = 100,
  resolution = 80,
  theme_settings = NULL,
  title = NA,
  show_time = FALSE,
  plot_original_platform = FALSE,
  original_platformx = NULL,
  original_platformy = NULL,
  original_platform_colour = "grey",
  original_platform_alpha = 0.4,
  original_platform_linetype = "dotted",
  original_platform_line_size = 0.5,
  original_platform_line_colour = "black"
)

Arguments

`data`	Data set containing at least following columns: "Time", "x", "y", "Animal", "Day", "Trial". "x" and "y" represent the coordinates (position) of the animal at a certain timepoint ("Time") during the trial.
`id`	ID of the animal
`day`	day number
`trial`	trial number
`centerx`	x coordinate of the center of the morris water maze (cm)
`centery`	y coordinate of the center of the morris water maze (cl)
`radius`	radius of the morris water maze (cm), default = 75
`platformx`	x coordinate of the center of the platform (cm)
`platformy`	y coordinate of the center of the platform (cm)
`platformradius`	radius of the platform (cm), default = 7.5
`ndata_circle`	Number of data points in the circle data set. Higher means smoother (more perfect) circle. Default = 100
`remove_data_outside_maze`	Remove datapoints that lie outside the water maze. Default = TRUE
`platform_colour`	Colour of the platform. Name or hexadecimal code (e.g.: #FF1020). Default = NA
`platform_alpha`	Alpha level for platform. Default = 1
`platform_linetype`	Linetype for platform. Derived from ggplot2. Default = "solid"
`platform_line_colour`	Colour of platform circle. Default = "black"
`platform_line_size`	Size of platform line. Default = 0.5
`heatmap_low`	Low range colour heatmap. Default = "yellow"
`heatmap_high`	High range colour heatmap. Default = "red"
`type`	Type of heatmap. Options are "raster" or "contour". Default = "raster"
`interpolate`	Interpolate raster heatmaps? Ignored for contour heatmaps. Default = TRUE
`contour_filled`	Fill contour heatmaps? Ignored for raster heatmaps. Default = TRUE
`contour_colour_scaled`	Colour scale for contour heatmaps. When false, colour of contour lines is set by contour_colour. When TRUE, colour scale is set by heatmap_low and heatmap_high. Default = FALSE
`contour_colour_filled`	Colour of contour lines in filled contour heatmap. Default = NA
`contour_colour`	Colour of contour lines in empty contour heatmap. Default = "blue"
`loop`	Loop the animation, default = FALSE
`width`	Width of the animation (px), default = 480
`height`	Height of the animation (px), default = 480
`duration`	Duration of the animation (s), default = 10
`frames`	Number of frames in the animation, default = 100
`resolution`	Resolution of GIF, passed to gifski. Default = 80
`theme_settings`	Optional parameter that passes list of arguments to ggplot2's theme() function.
`title`	Add title to GIF. Default = NA
`show_time`	Shows trial time(s) as subtitle (ggplot). Default = FALSE
`plot_original_platform`	Plot the original platform (for reversal trials). Default = FALSE
`original_platformx`	x coordinate of the center of the original platform (cm). Ignored if plot_original_platform = FALSE
`original_platformy`	y coordinate of the center of the original platform (cm). Ignored if plot_original_platform = FALSE
`original_platform_colour`	Colour of the original platform. Name or hexadecimal code (e.g.: #FF1020). Ignored if plot_original_platform = FALSE. Default = "grey"
`original_platform_alpha`	Alpha level for original platform. Ignored if plot_original_platform = FALSE. Default = 0.4
`original_platform_linetype`	Linetype of original platform circle. Ignored if plot_original_platform = FALSE. Default = "dotted"
`original_platform_line_size`	Size of original platform circle. Ignored if plot_original_platform = FALSE. Default = 0.5
`original_platform_line_colour`	Colour of original platform circle line. Ignored if plot_original_platform = FALSE. Default = "black"