46 lines
2.1 KiB
Python
46 lines
2.1 KiB
Python
# Copyright Spack Project Developers. See COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack.package import *
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class RDensvis(RPackage):
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"""Density-Preserving Data Visualization via Non-Linear Dimensionality
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Reduction.
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Implements the density-preserving modification to t-SNE and UMAP described
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by Narayan et al. (2020) . The non-linear dimensionality reduction
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techniques t-SNE and UMAP enable users to summarise complex
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high-dimensional sequencing data such as single cell RNAseq using lower
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dimensional representations. These lower dimensional representations enable
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the visualisation of discrete transcriptional states, as well as continuous
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trajectory (for example, in early development). However, these methods
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focus on the local neighbourhood structure of the data. In some cases, this
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results in misleading visualisations, where the density of cells in the
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low-dimensional embedding does not represent the transcriptional
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heterogeneity of data in the original high-dimensional space. den-SNE and
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densMAP aim to enable more accurate visual interpretation of
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high-dimensional datasets by producing lower-dimensional embeddings that
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accurately represent the heterogeneity of the original high-dimensional
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space, enabling the identification of homogeneous and heterogeneous cell
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states. This accuracy is accomplished by including in the optimisation
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process a term which considers the local density of points in the original
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high-dimensional space. This can help to create visualisations that are
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more representative of heterogeneity in the original high-dimensional
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space."""
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bioc = "densvis"
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license("MIT")
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version("1.10.0", commit="833db1fb7b2a5667575cc2e7c2fefc8360c8d7fb")
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depends_on("cxx", type="build") # generated
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depends_on("r-rcpp", type=("build", "run"))
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depends_on("r-basilisk", type=("build", "run"))
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depends_on("r-assertthat", type=("build", "run"))
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depends_on("r-reticulate", type=("build", "run"))
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depends_on("r-irlba", type=("build", "run"))
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