tests/testthat/test-plot_by_subject.R

In pathviewr: Wrangle, Analyze, and Visualize Animal Movement Data

#Tests of plot_by_subject()
library(ggplot2)
library(magrittr)

## test of object input
test_that("plot_by_subject() fails when data are missing or nonsense args",
          {
            expect_error(plot_by_subject(obj_name = "steve"))
            expect_error(plot_by_subject(col_by_treat = 1))
            expect_error(plot_by_subject())
          })

## Import the example Motive data included in the package
motive_data <-
  read_motive_csv(system.file("extdata", "pathviewr_motive_example_data.csv",
                              package = 'pathviewr'))

## Clean, isolate, and label trajectories
motive_full <-
  motive_data %>%
  clean_viewr(desired_percent = 50,
              max_frame_gap = "autodetect",
              span = 0.95)

#set axes limits based on data
height_limits <- c(max(abs(range(
  motive_full$position_height
))) * -1,
max(abs(range(
  motive_full$position_height
))))
width_limits <- c(max(abs(range(
  motive_full$position_width
))) * -1,
max(abs(range(
  motive_full$position_width
))))

#test axes limits
test_that("base functions set axes correctly", {
  expect_equal(max(abs(range(
    motive_full$position_height
  ))) * -1,-0.243158)
  expect_equal(max(abs(range(
    motive_full$position_width
  ))), width_limits[[2]])
})

# if (col_by_treat == FALSE)
#for top view
top_view <- motive_full %>%
  dplyr::group_by(subject) %>%
  tidyr::nest() %>%
  dplyr::mutate(
    paths = purrr::map(
      data,
      ~ ggplot2::ggplot(., aes(position_length,
                               position_width)) +
        geom_point(alpha = .1, show.legend = FALSE) +
        ylim(width_limits) +
        geom_hline(yintercept = 0, linetype = "dotted") +
        coord_fixed(ratio = 1)
    ),
    hist = purrr::map(
      data,
      ~ ggplot2::ggplot(., aes(x = position_width)) +
        geom_density(
          alpha = .5,
          position = "identity",
          show.legend = FALSE
        ) +
        xlim(width_limits) +
        geom_vline(xintercept = 0, linetype = "dotted") +
        coord_flip()
    )
  )
#all of them together:
top_all_plots <- top_view %>%
  dplyr::select(subject, paths, hist) %>%
  tidyr::gather("plot_type", "allplots", 2:3)

#test top views
test_that("top views created correctly via purrr::map", {
  expect_equal(top_view[[3]][[1]][["data"]][["position_width"]][[2]],-.1163564)
  # expect_equal(environment(top_view[[4]][[3]][["facet"]][["super"]])[["args"]],
  #              NULL)
})

test_that("top views wrangled correctly via tidyverse", {
  expect_match(top_all_plots$plot_type[[1]], "paths")
  expect_match(top_all_plots$subject[[5]], "device03")
  expect_match(top_all_plots[[3]][[4]][["labels"]][["x"]], "position_width")
})

#test that plotting works?
pdf(file = NULL)
plot_by_subject(motive_full,
                col_by_treat = FALSE)
dev.off()

#test plot output w/vdiffr
#plot_by_subject_default1 <- plot_by_subject(motive_full)[[1]]
#plot_by_subject_default2 <- plot_by_subject(motive_full)[[2]]
#use addins to open shiny app to validate plots
# test_that("plot_by_subject() default plot output is OK", {
#   skip_on_cran()
#   skip_on_travis()
#   skip_on_appveyor()
#   skip_on_gh_actions
#   vdiffr::expect_doppelganger("plot by subject default 1",
#                               plot_by_subject_default1)
#   vdiffr::expect_doppelganger("plot by subject default 2",
#                               plot_by_subject_default2)
# })

## Add treatment information
motive_full$treatment <- c(rep("latA", 100),
                           rep("latB", 100),
                           rep("latA", 100),
                           rep("latB", 149))

#if (col_by_treat == TRUE)
#for elev view (change in height):
elev_view <- motive_full %>%
  dplyr::group_by(subject) %>%
  tidyr::nest() %>%
  dplyr::mutate(
    paths = purrr::map(
      data,
      ~ ggplot2::ggplot(., aes(
        position_length, position_height, colour = treatment
      )) +
        geom_point(alpha = .1, show.legend = FALSE) +
        ylim(height_limits) +
        geom_hline(yintercept = 0, linetype = "dotted") +
        coord_fixed(ratio = 1)
    ),
    hist = purrr::map(
      data,
      ~ ggplot2::ggplot(., aes(position_height, fill = treatment)) +
        geom_density(
          alpha = .5,
          position = "identity",
          show.legend = FALSE
        ) +
        xlim(height_limits) +
        geom_vline(xintercept = 0, linetype = "dotted") +
        coord_flip()
    )
  )

#all of them together:
elev_all_plots <- elev_view %>%
  dplyr::select(subject, paths, hist) %>%
  tidyr::gather("plot_type", "allplots", 2:3)

#test elev views
test_that("elev views created correctly via purrr::map", {
  expect_equal(
    elev_view[[3]][[1]][["data"]][["position_width"]][[98]],-0.09991182)
  # expect_equal(environment(elev_view[[4]][[3]][["facet"]][["super"]])[["args"]],
  #              NULL)
})

test_that("elev views wrangled correctly via tidyverse", {
  expect_match(elev_all_plots$plot_type[[3]], "paths")
  expect_match(elev_all_plots$subject[[4]], "device02")
  expect_match(elev_all_plots[[3]][[4]][["labels"]][["x"]], "position_height")
})

## Test that plotting works?
pdf(file = NULL)
plot_by_subject(motive_full,
                col_by_treat = TRUE)
dev.off()

## Test arguments to plot_by_subject()
test_that("plot_by_subject() fails when nonsense is supplied", {
  expect_error(plot_by_subject(motive_full,
                               col_by_treat = jobin))
})

# #test plot output w/vdiffr
#   plot_by_subject_colbytreat1 <-
#     plot_by_subject(motive_full, col_by_treat = TRUE)[[1]]
#   plot_by_subject_colbytreat2 <-
#     plot_by_subject(motive_full, col_by_treat = TRUE)[[2]]
# #use addins to open shiny app to validate plots
# test_that("plot_by_subject() col_by_treat plot output is OK", {
#   skip_on_cran()
#   skip_on_travis()
#   skip_on_appveyor()
#   skip_on_gh_actions
#   vdiffr::expect_doppelganger("plot by subject colbytreat 1",
#                               plot_by_subject_colbytreat1)
#   vdiffr::expect_doppelganger("plot by subject colbytreat 2",
#                               plot_by_subject_colbytreat2)
# })