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Plot the time-series depth records of the days closest to the centre of each cluster

Source: R/10_plot_clusters.R
plot_clusters.Rd

plot_clusters plots the time-depth records of the days closest to the centre of each of the clusters. Each cluster is plotted both individually, and faceted together, with both a fixed y-axis and a free y-axis (depth).

Usage

plot_clusters(
  tag_vector = tag_list,
  data_folder = NULL,
  kmeans_result,
  No_days = 1,
  every_nth = 10,
  every_s = 0,
  Y_lim = c(0, 250, 50),
  color = TRUE,
  diel_shade = FALSE,
  dpi = 300,
  output = FALSE,
  output_folder = NULL,
  verbose = FALSE
)

Arguments

tag_vector

A character vector of tag IDs. E.g. 'c("123456", "456283", "AB98XJ").

data_folder

Parent folder path with separate folders for each tag data. E.g. "C:/Tag data". Defaults to 'data_dir'

kmeans_result

An object of class 'kmeans' containing the k-means clustering data. Output of 'k_clustering()' function.

No_days

Numerical. Number of days of each cluster to plot. Defaults to 1.

every_nth

Numerical. Optional down-sampling of data points to plot. Defaults to 10, plotting every 10th record.

every_s

Numerical. Alternative to every_nth. Optional down-sampling of data points to plot by number of seconds, as opposed to records. E.g. plots every 60th second, rather than 10th row of data. Must be a multiple of the sampling frequency. Overrides every_nth if != 0.

Y_lim

Character vector with minimum depth, maximum depth, and sequence for ticks on Y-axis. Must be numeric, positive and 3 elements long. E.g. c(0,1500,100).

color

TRUE or FALSE. Output clusters coloured by cluster assignment. Defaults to TRUE.

diel_shade

TRUE or FALSE. Output plot with night-time shading. Can be slow! Defaults to FALSE.

dpi

Numerical. DPI to use for 'ggsave()' output. E.g, 600

output

Logical. If TRUE, output is saved to output_folder. Defaults to FALSE.

output_folder

Output folder path. If output = TRUE, output_folder must be provided. Defaults to NULL.

verbose

Logical. If TRUE, progress messages are shown. Defaults to FALSE.

Value

A plot list of all plots created of each cluster in the data. When output == TRUE this prints to file one figure for each Cluster with a fixed y-axis. Additionally outputs a facet plot of all clusters, and a free y-axis version of all plots.

Examples

# Set file path
filepath <- system.file("extdata", package = "FishDiveR")

# Load kmeans_result
kmeans_result <- readRDS(file.path(filepath, "data/5_k-means/kmeans_result.rds"))

# Run plot_clusters function
plot_clusters(
  tag_vector = "data",
  data_folder = filepath,
  kmeans_result = kmeans_result,
  No_days = 1,
  every_nth = 10,
  every_s = 0,
  Y_lim = c(0, 300, 50),
  color = TRUE,
  diel_shade = FALSE,
  dpi = 100,
  output = TRUE,
  output_folder = tempdir(),
  verbose = TRUE
)
#> Maximum depth is 262.2
#> Data sampling interval is 60 seconds
#> Plotting every 10 records
#> Cluster 1 dates 2000-01-08 Tag: data
#> Cluster 2 dates 2000-01-10 Tag: data
#> Cluster 3 dates 2000-01-03 Tag: data
#> Cluster 4 dates 2000-01-04 Tag: data
#> Output folder: /tmp/RtmpTKWEE7/data/6_Cluster-plots.K=4
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