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General interactivity

General-interactivity.Rmd

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.

  • Feature selection
  • Subset selection and highlighting
  • Resetting to original subsets
  • Updating currently displayed projection frames
  • Changing the number of bins of histograms
  • Animating the currently loaded tours
  • Setting a threshold for blending projection axes with a low length out
  • Saving and loading the state of the GUI
  • Initiating new tours

Examples for all displays can be found below.

Setup 

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

# Initialize python backend
init_env()

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()))
grand_tour_history_1d <- save_history(data,
                                      tour_path=grand_tour(d=1))

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

init_env()

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")

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.

Feature selection demo
Feature selection demo

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.

Subset selection and highlighting demo
Subset selection and highlighting demo

Resetting to original subsets

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

Subset resetting demo
Subset resetting demo

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 texboxes and clicking the “Update frames” button. Updating the frames can also ben 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.

Update frames demo
Update frames demo

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.

Update number of bins demo
Update number of bins demo

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.

Animate tours demo
Animate tours demo

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.

Projection axes blend out demo
Projection axes blend out demo

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

  • a .png file containing the currently displayed graphics
  • .csv files that capture the feature and subset selection as well as projections of the tours displayed at the time of the snapshot
  • two .pkl files that contain state features of the GUI, allowing for complete recovery of the saved state

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

Save and load GUI state demo
Save and load GUI state demo

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.

Save projections and subsets demo
Save projections and subsets demo