General Interactivity

Overview

The lionfish package offers multiple different types of general interactivity. The following operations can be performed with the elements on the frame on the left.

Examples for all displays can be found below.

Setup

# Load required packages
library(tourr)
library(lionfish)

# Initialize python backend
if (check_venv()){
init_env(env_name = "r-lionfish", virtual_env = "virtual_env")
} else if (check_conda_env()){
init_env(env_name = "r-lionfish", virtual_env = "anaconda")
}
#> Using virtual environment 'r-lionfish' ...
#> + /home/matthias/.virtualenvs/r-lionfish/bin/python -m pip install --upgrade --no-user 'numpy>=2.0'
#> Python environment "r-lionfish" successfully loaded

Dataset - Flea data

data("flea")
data <- apply(flea[,1:6], 2, function(x) (x-mean(x))/sd(x))
clusters <- as.numeric(flea$species)
flea_subspecies <- unique(flea$species)

guided_tour_history <- save_history(data,
                                    tour_path=guided_tour(holes()))
#> Target: 1.181, 19.0% better
#> Target: 1.221, 3.4% better
#> Target: 1.252, 2.5% better
#> Target: 1.255, 0.3% better
#> Target: 1.260, 0.4% better
#> Target: 1.266, 0.4% better
#> Target: 1.275, 0.7% better
#> Target: 1.276, 0.1% better
#> Target: 1.278, 0.1% better
#> No better bases found after 25 tries.  Giving up.
#> Final projection:
#> -0.062   0.661
#>  0.534   0.377
#>  0.428   0.062
#>  0.550  -0.117
#> -0.006   0.584
#>  0.475  -0.249
grand_tour_history_1d <- save_history(data,
                                      tour_path=grand_tour(d=1))

half_range <- max(sqrt(rowSums(data^2)))
feature_names <- colnames(data)

obj1 <- list(type="2d_tour", obj=guided_tour_history)
obj2 <- list(type="1d_tour", obj=grand_tour_history_1d)
obj3 <- list(type="scatter", obj=c("tars1", "tars2"))
obj4 <- list(type="hist", obj="head")

if (check_venv()){
init_env(env_name = "r-lionfish", virtual_env = "virtual_env")
} else if (check_conda_env()){
init_env(env_name = "r-lionfish", virtual_env = "anaconda")
}
#> Using virtual environment 'r-lionfish' ...
#> + /home/matthias/.virtualenvs/r-lionfish/bin/python -m pip install --upgrade --no-user 'numpy>=2.0'
#> Python environment "r-lionfish" successfully loaded
  
  
if (interactive()){
interactive_tour(data=data,
                 plot_objects=list(obj1, obj2, obj3, obj4),
                 feature_names=feature_names,
                 half_range=half_range,
                 n_plot_cols=2,
                 preselection=clusters,
                 preselection_names=flea_subspecies,
                 n_subsets=5,
                 display_size=4.5)
}

Currently supported general interactivity

Feature selection

A list of all features can be found on the top left. Each feature has a checkbox next to it. The features are selected or deselected by checking or unchecking the respective checkboxes.

Subset selection and highlighting

A list of all subsets can be found below the features. Each subset has a checkbox next to it. The subsets are selected checking respective checkboxes next to them. When a subset is active, all datapoints that are selected with one of the interactive plots will be moved to that subset. The colored patches next to the subsets indicate the color of the datapoints within the respective subset. The transparency of the datapoints of the subsets can be changed by clicking the colored patches next to the subset names. The names of the subsets can be changed by writing in the textboxes.

Resetting to original subsets

The current subset selection can easily be reset by clicking the “Reset original selection” button.

Updating currently displayed projection frames

One can jump between frames of tours by typing the desired frame one wants to jump to into the corresponding textboxes and clicking the “Update frames” button. Updating the frames can also be useful if some of the plots haven’t updated properly or one wants to reset the shown projections of a frame after manipulation of the projection axes.

Changing the number of bins of histograms

The number of bins of histograms can be changed by typing the desired number of bins in the corresponding textbox. A larger number of bins results in a higher resolution, but it will increase the time it takes to update histograms due the increased computational load.

Animating the currently loaded tours

The currently loaded tours can be animated by checking the checkbox below the “Update frames” button. The interval in which the next frames will be loaded can be changed in the textbox next to the checkbox.

Setting a threshold for blending projection axes with a low length out

If there are many projection axes displayed it can clutter the plot. To combat this the option to blend out projection axes of low length has been implemented. Therefore, a projection threshold (a float between 0 and 1) can be set and by checking the checkbox, projection axes that are shorter than the threshold are blended out.

Saving and loading the state of the GUI

The current state of the GUI can be saved by clicking the “Save projections and subsets” button. This will produce a file browser with which one can choose the directory for the files to be saved in. The saved files are

Alternatively the function load_interactive_tour() can be used to load a save directly.

Initiating new tours

New tours can be initiated by first choosing what tour one wants to compute and then pressing “Run tour”. Currently, local tours and guided tours with the indices holes and LDA are available. Local tours will be initiated with the currently displayed projections. They can therefore be used to further explore projections similar to the displayed one. By pressing “Reset original tour” one can return to the originally loaded tours.