All Available Views

“What is to be sought in designs for the display of information is the clear portrayal of complexity. Not the complication of the simple; rather the task of the designer is to give visual access to the subtle and the difficult - that is, the revelation of the complex.”

-Edward Tufte

Introduction

In this vignette, we introduce the trellis_viz() function and show all of the available visualizations in PreciseDist. The trellis_viz() function is simply a wrapper around precise_viz() that allows multiple visualizations to be calculated and viewed at once. Unlike precise_viz(), however, trellis_viz() outputs a html folder and nothing else. The Index.html file within that folder is where the output visualization lies.

Also, a few things to note about the below commands:

Data and set-up comes from the Cell Cycle Vignette - Experiment 5: Minkowski 100x. See that vignette for more details.
Note the self_contained = TRUE option in trellis_viz(). This typically (but mysteriously, not always) needs to be set to TRUE for inclusion into interactive Rmarkdown documents etc.
The trelliscope library is very interactive as are the plots contained within! Make sure to mouse over the plots to test their interactivity and to scroll though the different plots and play with the grid option and other options on the sidebar if you have never seen this visualization before.

Data set-up

library(PreciseDist)
data("data_cell_cycle")
str(data_cell_cycle[1:5])
library(dplyr)
cell_cycle_data <- data_cell_cycle %>%
  dplyr::select(-Cell_cycle) %>%
  as.matrix()
cell_cycle_labels <- data_cell_cycle %>%
  dplyr::select(Cell_cycle) %>%
  as.matrix()
cell_cycle_minkowski_params <- seq(0.45, 0.54, length.out = 10)
cell_cycle_minkowski_funcs <- precise_func_fact(
  func = "minkowski",
  params = cell_cycle_minkowski_params
)
library(future)
library(doFuture)
registerDoFuture()
plan(multiprocess, workers = 10)
cell_cycle_minkowski_dists <- cell_cycle_data %>%
  as.matrix() %>%
  precise_dist(
    dist_funcs = cell_cycle_minkowski_funcs,
    time_series = FALSE,
    partitions = 10,
    suffix = "cell_minkowski_",
    file = "/absolute_path/to_somewhere/with_full_name/inclusing_the/file_extension.rds",
    parallel = TRUE,
    local_timeout = Inf,
    verbose = TRUE
  )
cell_cycle_minkowski_transformed <- cell_cycle_minkowski_dists  %>%
  precise_transform(transform = "laplacian")
cell_cycle_minkowski_fused <- precise_fusion(
  cell_cycle_minkowski_transformed,
  fusion = "fuse",
  verbose = TRUE
)
cell_cycle_minkowski_graph <- precise_graph(
  data = cell_cycle_minkowski_fused,
  method = 1,
  n_neighbors = 50,
  spread = 10,
  min_dist = 0.001,
  bandwidth = 10,
  parallel = TRUE,
  verbose = TRUE
)

2D Graphs

library(future)
library(doFuture)
registerDoFuture()
plan(multicore, workers = 10)
trellis_viz(
  data = cell_cycle_minkowski_graph,
  path = "/absolute_path/to_somewhere/with_full_name/not_including_a/file_extension",
  name = "Graphs_and_Plots",
  plot_type = "2d_graphs",
  color_vec = as.character(cell_cycle_labels),
  colors = c("#0017FF", "#000000", "#FF0017"),
  size = 0.5,
  self_contained = TRUE,
  group = "common",
  desc = "",
  md_desc = "",
  height = 500,
  width = 500,
  nrow = 2,
  ncol = 3,
  parallel = TRUE,
  verbose = TRUE
)

2D Scatterplots

library(future)
library(doFuture)
registerDoFuture()
plan(multicore, workers = 10)
trellis_viz(
  data = cell_cycle_minkowski_graph,
  path = "/absolute_path/to_somewhere/with_full_name/not_including_a/file_extension",
  name = "Graphs_and_Plots",
  plot_type = "2d_plots",
  color_vec = as.character(cell_cycle_labels),
  colors = c("#0017FF", "#000000", "#FF0017"),
  size = 0.5,
  self_contained = TRUE,
  group = "common",
  desc = "",
  md_desc = "",
  height = 500,
  width = 500,
  nrow = 2,
  ncol = 3,
  parallel = TRUE,
  verbose = TRUE
)

3D Graphs

library(future)
library(doFuture)
registerDoFuture()
plan(multicore, workers = 6)
trellis_viz(
  data = cell_cycle_minkowski_graph,
  path = "/absolute_path/to_somewhere/with_full_name/not_including_a/file_extension",
  name = "Graphs_and_Plots",
  plot_type = "3d_graphs",
  color_vec = as.character(cell_cycle_labels),
  colors = c("#0017FF", "#000000", "#FF0017"),
  size = 0.5,
  self_contained = TRUE,
  group = "common",
  desc = "",
  md_desc = "",
  height = 500,
  width = 500,
  nrow = 2,
  ncol = 3,
  parallel = TRUE,
  verbose = TRUE
)

3D Scatterplots

library(future)
library(doFuture)
registerDoFuture()
plan(multicore, workers = 6)
trellis_viz(
  data = cell_cycle_minkowski_graph,
  path = "/absolute_path/to_somewhere/with_full_name/not_including_a/file_extension",
  name = "Graphs_and_Plots",
  plot_type = "3d_plots",
  color_vec = as.character(cell_cycle_labels),
  colors = c("#0017FF", "#000000", "#FF0017"),
  size = 0.5,
  self_contained = TRUE,
  group = "common",
  desc = "",
  md_desc = "",
  height = 500,
  width = 500,
  nrow = 2,
  ncol = 3,
  parallel = TRUE,
  verbose = TRUE
)

Brian Muchmore