Plot individual map

Plot individual map

Usage

plot_ind_mitemap(
  MiteMap,
  file_names = NULL,
  ind_index = c(1),
  time_animation = FALSE,
  add_base_circle = FALSE,
  add_odor_source = TRUE,
  label_odor_source = NULL,
  center_base_circle = c(0, 0),
  breaks_animation = 10,
  diameter_base_circle = 40,
  npoints_base_circle = 100,
  linewidth = 1.2,
  alpha_shadow = 0.4
)

Arguments

MiteMap

MiteMap (required) The result of import_mitemap ($resulting_data) for raw_data

file_names

(vector of string, default = NULL) The names of the file(s) (individual(s)) you want to plot (e.g. c("MM012022_05_17_13h25m12s", "MM012022_05_17_09h23m48s")). If not NULL, ind_index is ignored.

ind_index

(vector of int, default = c(1)) The index numbers of the file(s) (individual(s)) you want to plot

time_animation

(logical, default FALSE) Does the plot is animate using gganimate ?#'

add_base_circle

(logical, default FALSE) Does the base circle is plot ?

add_odor_source

(logical, default TRUE) Does the odor source is plot ?

label_odor_source

(string, default = NULL) Label of the odor source. Only used if add_odor_source is TRUE. If NULL, no label is added.

center_base_circle

(int) The center of the base circle. Only used if center_base_circle is TRUE.

breaks_animation

(int) The number of breaks in animation. Only used if time_animation is TRUE.

diameter_base_circle

(int) The diameter of the base circle. Only used if center_base_circle is TRUE.

npoints_base_circle

(int) The number of point to draw the base circle. Only used if center_base_circle is TRUE.

linewidth

(int) The linewidth of the path

alpha_shadow

(int [0,1]) Alpha value (transparency) for shadow path. Only used if time_animation` is TRUE.

Value

A list of ggplot object

Author

Adrien Taudière

Examples

MM <- import_mitemap(
  system.file("extdata", "mitemap_example", package = "MiteMapTools"),
  file_name_column = "File (mite ID)",
  verbose = FALSE
)

library(patchwork)
p <- plot_ind_mitemap(MM, file_names = c("MM012022_05_17_13h22m59s", "MM012022_05_17_08h23m05s"))
p[[1]] + p[[2]] & theme(legend.position = "none")



p_l <- plot_ind_mitemap(MM, ind_index = c(1, 2))
p_l[[1]] + p_l[[2]] & theme(legend.position = "none")


p_l_base_c <- plot_ind_mitemap(MM,
  add_base_circle = TRUE, linewidth = 1.7,
  label_odor_source = "Odor source"
)
p_l_base_c[[1]] + scale_color_gradient(name = "Speed", trans = "log10", low = "cyan", high = "red")
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
#> Warning: log-10 transformation introduced infinite values.


if (!requireNamespace("gganimate", quietly = TRUE)) {
  p_l_anim <- plot_ind_mitemap(MM, time_animation = TRUE, breaks_animation = 15)
  p_l_anim[[1]]

  p_l <- plot_ind_mitemap(MM, ind_index = c(1:6))
  (p_l[[1]] + p_l[[2]] + p_l[[3]]) /
    (p_l[[4]] + p_l[[5]] + p_l[[6]]) +
    plot_layout(guides = "collect") & scale_color_gradient(
    name = "Speed", trans = "log1p", low = "cyan", high = "red",
    limits = c(
      min(unlist(lapply(p_l, function(x) {
        min(x$data$dist_from_i_minus_1, na.rm = T)
      }))),
      max(unlist(lapply(p_l, function(x) {
        max(x$data$dist_from_i_minus_1, na.rm = T)
      })))
    )
  )

  (p_l[[1]] + p_l[[2]] + p_l[[3]]) /
    (p_l[[4]] + p_l[[5]] + p_l[[6]]) +
    plot_layout(guides = "collect") &
    scale_color_viridis_c(name = "Speed", trans = "log1p", limits = c(0, 2))
}