Package: quollr 0.2.0

quollr: Visualising How Nonlinear Dimension Reduction Warps Your Data

To construct a model in 2D space from 2D embedding data and then lift it to the high-dimensional space. Additionally, it provides tools to visualize the model in 2D space and to overlay the fitted model on data using the tour technique. Furthermore, it facilitates the generation of summaries of high-dimensional distributions.

Authors:Jayani P.G. Lakshika [aut, cre], Dianne Cook [aut], Paul Harrison [aut], Michael Lydeamore [aut], Thiyanga S. Talagala [aut]

quollr_0.2.0.tar.gz
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quollr.pdf |quollr.html✨
quollr/json (API)
NEWS

# Install 'quollr' in R:
install.packages('quollr', repos = c('https://jayanilakshika.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jayanilakshika/quollr/issues

Datasets:

On CRAN:

6.26 score 3 stars 7 scripts 156 downloads 32 exports 86 dependencies

Last updated 10 days agofrom:ee43798601. Checks:3 OK, 2 NOTE, 3 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 07 2025
R-4.5-winERRORFeb 09 2025
R-4.5-macNOTEFeb 07 2025
R-4.5-linuxNOTEFeb 07 2025
R-4.4-winERRORFeb 09 2025
R-4.4-macOKFeb 07 2025
R-4.3-winERRORFeb 09 2025
R-4.3-macOKFeb 07 2025

Exports:assign_dataaugmentavg_highd_datacal_2d_distcalc_bins_ycompute_mean_density_hexcompute_std_countsextract_hexbin_centroidsextract_hexbin_meanfind_lg_benchmarkfind_low_dens_hexfind_non_empty_binsfind_ptsfit_highd_modelgen_centroidsgen_edgesgen_hex_coordgen_proj_langevitourgen_scaled_datageom_hexgridgeom_trimeshget_min_indicesglancehex_binningpredict_embshow_langevitourshow_link_plotsstat_hexgridstat_trimeshtri_bin_centroidsvis_lg_meshvis_rmlg_mesh

Dependencies:askpassassertthatbase64encbslibcachemclicodetoolscolorspacecpp11crosstalkcurldata.tabledeldirdigestdplyrevaluatefansifarverfastmapfontawesomefsfurrrfuturegenericsggplot2globalsgluegtablehighrhtmltoolshtmlwidgetshttrinterpisobandjquerylibjsonliteknitrlabelinglangevitourlaterlatticelazyevallifecyclelistenvmagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslparallellypillarpkgconfigplotlypromisesproxypurrrR6RANNrappdirsRColorBrewerRcppRcppEigenrlangrmarkdownrsamplesassscalessliderstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewarpwithrxfunyaml

Data preprocessing

Rendered fromquollr1dataprocessing.Rmdusingknitr::rmarkdownon Feb 07 2025.

Last update: 2024-05-08
Started: 2024-02-29

Algorithm for visualising the model overlaid on high-dimensional data

Rendered fromquollr2algo.Rmdusingknitr::rmarkdownon Feb 07 2025.

Last update: 2024-05-17
Started: 2024-02-29

Algorithm for binning data

Rendered fromquollr3hexbin.Rmdusingknitr::rmarkdownon Feb 07 2025.

Last update: 2024-07-22
Started: 2024-02-29

Generating model summaries

Rendered fromquollr4summary.Rmdusingknitr::rmarkdownon Feb 07 2025.

Last update: 2024-05-13
Started: 2024-02-29

Quick start

Rendered fromquollr5quickstart.Rmdusingknitr::rmarkdownon Feb 07 2025.

Last update: 2024-05-16
Started: 2024-03-19

Readme and manuals

Help Manual

Help pageTopics
Assign data to hexagonsassign_data
Augment Data with Predictions and Error Metricsaugment
Create a dataframe with averaged high-dimensional dataavg_highd_data
Calculate 2D Euclidean distances between verticescal_2d_dist
Calculate the effective number of bins along x-axis and y-axiscalc_bins_y
Compute mean density of hexagonal binscompute_mean_density_hex
Compute standardize counts in hexagonscompute_std_counts
Extract hexagonal bin centroids coordinates and the corresponding standardise counts.extract_hexbin_centroids
Extract hexagonal bin mean coordinates and the corresponding standardize counts.extract_hexbin_mean
Compute a benchmark value to remove long edgesfind_lg_benchmark
Find low-density Hexagonsfind_low_dens_hex
Find the number of bins required to achieve required number of non-empty bins.find_non_empty_bins
Find points in hexagonal binsfind_pts
Construct the 2D model and lift into high-Dfit_highd_model
Generate centroid coordinategen_centroids
Generate edge informationgen_edges
Generate hexagonal polygon coordinatesgen_hex_coord
Visualize a specific projection of langevitourgen_proj_langevitour
Scaling the NLDR datagen_scaled_data
Create a hexgrid plotgeom_hexgrid
Create a trimesh plotgeom_trimesh
GeomHexgrid: A Custom ggplot2 Geom for Hexagonal GridGeomHexgrid
GeomTrimesh: A Custom ggplot2 Geom for Triangular MeshesGeomTrimesh
Get indices of all minimum distancesget_min_indices
Generate evaluation metricsglance
Hexagonal binninghex_binning
Predict 2D embeddingspredict_emb
S-curve dataset with noise dimensionss_curve_noise
S-curve dataset with noise dimensions for tests_curve_noise_test
S-curve dataset with noise dimensions for trainings_curve_noise_training
UMAP embedding for S-curve dataset which with noise dimensionss_curve_noise_umap
Predicted UMAP embedding for S-curve dataset which with noise dimensionss_curve_noise_umap_predict
Scaled UMAP embedding for S-curve dataset which with noise dimensionss_curve_noise_umap_scaled
Visualize the model overlaid on high-dimensional datashow_langevitour
Visualize the model overlaid on high-dimensional data along with 2D wireframe model.show_link_plots
stat_hexgrid Custom Stat for hexagonal grid plotstat_hexgrid
stat_trimesh Custom Stat for trimesh plotstat_trimesh
Triangulate bin centroidstri_bin_centroids
Visualize triangular mesh with coloured long edgesvis_lg_mesh
Visualize triangular mesh after removing the long edgesvis_rmlg_mesh