Package: EmbedSOM 2.1.2

EmbedSOM: Fast Embedding Guided by Self-Organizing Map

Provides a smooth mapping of multidimensional points into low-dimensional space defined by a self-organizing map. Designed to work with 'FlowSOM' and flow-cytometry use-cases. See Kratochvil et al. (2019) <doi:10.12688/f1000research.21642.1>.

Authors:Mirek Kratochvil [aut, cre], Sofie Van Gassen [cph], Britt Callebaut [cph], Yvan Saeys [cph], Ron Wehrens [cph]

EmbedSOM_2.1.2.tar.gz
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EmbedSOM.pdf |EmbedSOM.html✨
EmbedSOM/json (API)

# Install 'EmbedSOM' in R:

install.packages('EmbedSOM', repos = c('https://exaexa.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/exaexa/embedsom/issues

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cytometry som visualization

5.70 score 25 stars 8 scripts 277 downloads 4 mentions 23 exports 53 dependencies

Last updated 2 years agofrom:d8476c145f. Checks:OK: 1 WARNING: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 25 2024
R-4.5-win-x86_64	WARNING	Oct 25 2024
R-4.5-linux-x86_64	WARNING	Oct 25 2024
R-4.4-win-x86_64	WARNING	Oct 25 2024
R-4.4-mac-x86_64	WARNING	Oct 25 2024
R-4.4-mac-aarch64	WARNING	Oct 25 2024
R-4.3-win-x86_64	WARNING	Oct 25 2024
R-4.3-mac-x86_64	WARNING	Oct 25 2024
R-4.3-mac-aarch64	WARNING	Oct 25 2024

Exports:ClusterPalette EmbedSOM ExprColors ExpressionGradient ExpressionPalette GQTSOM GraphCoords Initialize_PCA kMeansMap kNNCoords MapDataToCodes MSTCoords NormalizeColor PlotData PlotDefault PlotEmbed PlotGG RandomMap SOM tSNECoords UMAPCoords UMatrixCoords uwotCoords

Dependencies:askpass BH cli colorspace cpp11 dqrng fansi farver FNN ggplot2 glue gtable here igraph irlba isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nlme openssl pillar pkgconfig png R6 rappdirs RColorBrewer Rcpp RcppAnnoy RcppEigen RcppProgress RcppTOML reticulate rlang rprojroot RSpectra Rtsne scales sitmo sys tibble umap utf8 uwot vctrs viridisLite withr

EmbedSOM basic embedding

Mirek Kratochvil

Rendered fromUsingEmbedSOM.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2020-01-18
Started: 2019-12-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
An acceptable cluster color palette	ClusterPalette
Process the cells with SOM into a nice embedding	EmbedSOM
Generate colors for multi-color marker expression labeling in a single plot	ExprColors
The ggplot2 scale gradient from ExpressionPalette.	ExpressionGradient
Marker expression palette generator based off ColorBrewer's RdYlBu, only better for plotting of half-transparent cells	ExpressionPalette
Train a Growing Quadtree Self-Organizing Map	GQTSOM
Add Kamada-Kawai-generated embedding coordinates to the map	GraphCoords
Create a grid from first 2 PCA components	Initialize_PCA
Create a map from k-Means clusters	kMeansMap
Add KNN-topology-based embedding coordinates to the map	kNNCoords
Assign nearest node to each datapoint	MapDataToCodes
Add MST-style embedding coordinates to the map	MSTCoords
Helper for computing colors for embedding plots	NormalizeColor
Export a data frame for plotting with marker intensities and density.	PlotData
Default plot	PlotDefault
Helper function for plotting the embedding	PlotEmbed
Wrap PlotData result in ggplot object.	PlotGG
Identity on whatever	PlotId
Create a map by randomly selecting points	RandomMap
Build a self-organizing map	SOM
Add tSNE-based coordinates to a map	tSNECoords
Add UMAP-based coordinates to a map	UMAPCoords
Add U-Matrix-optimized embedding coordinates to the map	UMatrixCoords
Add UMAP-based coordinates to a map, using the 'uwot' package	uwotCoords