1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
|
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class RDensvis(RPackage):
"""Density-Preserving Data Visualization via Non-Linear Dimensionality
Reduction.
Implements the density-preserving modification to t-SNE and UMAP described
by Narayan et al. (2020) . The non-linear dimensionality reduction
techniques t-SNE and UMAP enable users to summarise complex
high-dimensional sequencing data such as single cell RNAseq using lower
dimensional representations. These lower dimensional representations enable
the visualisation of discrete transcriptional states, as well as continuous
trajectory (for example, in early development). However, these methods
focus on the local neighbourhood structure of the data. In some cases, this
results in misleading visualisations, where the density of cells in the
low-dimensional embedding does not represent the transcriptional
heterogeneity of data in the original high-dimensional space. den-SNE and
densMAP aim to enable more accurate visual interpretation of
high-dimensional datasets by producing lower-dimensional embeddings that
accurately represent the heterogeneity of the original high-dimensional
space, enabling the identification of homogeneous and heterogeneous cell
states. This accuracy is accomplished by including in the optimisation
process a term which considers the local density of points in the original
high-dimensional space. This can help to create visualisations that are
more representative of heterogeneity in the original high-dimensional
space."""
bioc = "densvis"
license("MIT")
version("1.10.0", commit="833db1fb7b2a5667575cc2e7c2fefc8360c8d7fb")
depends_on("r-rcpp", type=("build", "run"))
depends_on("r-basilisk", type=("build", "run"))
depends_on("r-assertthat", type=("build", "run"))
depends_on("r-reticulate", type=("build", "run"))
depends_on("r-irlba", type=("build", "run"))
|
