1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
4 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
6 ;;; This file is part of GNU Guix.
8 ;;; GNU Guix is free software; you can redistribute it and/or modify it
9 ;;; under the terms of the GNU General Public License as published by
10 ;;; the Free Software Foundation; either version 3 of the License, or (at
11 ;;; your option) any later version.
13 ;;; GNU Guix is distributed in the hope that it will be useful, but
14 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
15 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16 ;;; GNU General Public License for more details.
18 ;;; You should have received a copy of the GNU General Public License
19 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
21 (define-module (gnu packages graph)
22 #:use-module (guix download)
23 #:use-module (guix git-download)
24 #:use-module (guix packages)
25 #:use-module (guix build-system gnu)
26 #:use-module (guix build-system python)
27 #:use-module (guix build-system r)
28 #:use-module ((guix licenses) #:prefix license:)
29 #:use-module (gnu packages)
30 #:use-module (gnu packages gcc)
31 #:use-module (gnu packages bioconductor)
32 #:use-module (gnu packages bioinformatics)
33 #:use-module (gnu packages compression)
34 #:use-module (gnu packages cran)
35 #:use-module (gnu packages graphviz)
36 #:use-module (gnu packages maths)
37 #:use-module (gnu packages multiprecision)
38 #:use-module (gnu packages pkg-config)
39 #:use-module (gnu packages python)
40 #:use-module (gnu packages python-web)
41 #:use-module (gnu packages python-xyz)
42 #:use-module (gnu packages statistics)
43 #:use-module (gnu packages time)
44 #:use-module (gnu packages xml))
53 (uri (string-append "http://igraph.org/nightly/get/c/igraph-"
57 "1pxh8sdlirgvbvsw8v65h6prn7hlm45bfsl1yfcgd6rn4w706y6r"))))
58 (build-system gnu-build-system)
61 (list "--with-external-glpk"
62 "--with-external-blas"
63 "--with-external-lapack")))
69 ("openblas" ,openblas)
71 (home-page "http://igraph.org")
72 (synopsis "Network analysis and visualization")
74 "This package provides a library for the analysis of networks and graphs.
75 It can handle large graphs very well and provides functions for generating
76 random and regular graphs, graph visualization, centrality methods and much
78 (license license:gpl2+)))
80 (define-public python-igraph
81 (package (inherit igraph)
82 (name "python-igraph")
83 (version "0.7.1.post6")
87 (uri (pypi-uri "python-igraph" version))
90 "0xp61zz710qlzhmzbfr65d5flvsi8zf2xy78s6rsszh719wl5sm5"))))
91 (build-system python-build-system)
94 `(("igraph" ,igraph)))
96 `(("pkg-config" ,pkg-config)))
97 (home-page "http://pypi.python.org/pypi/python-igraph")
98 (synopsis "Python bindings for the igraph network analysis library")))
100 (define-public r-igraph
107 (uri (cran-uri "igraph" version))
110 "1jwjjl0l4054w05bik17p2d6rj3lx68iv716phajhnbbmckfnj0h"))))
111 (build-system r-build-system)
113 `(("gfortran" ,gfortran)))
120 `(("r-magrittr" ,r-magrittr)
121 ("r-matrix" ,r-matrix)
122 ("r-pkgconfig" ,r-pkgconfig)))
123 (home-page "http://igraph.org")
124 (synopsis "Network analysis and visualization")
126 "This package provides routines for simple graphs and network analysis.
127 It can handle large graphs very well and provides functions for generating
128 random and regular graphs, graph visualization, centrality methods and much
130 (license license:gpl2+)))
132 (define-public r-diffusionmap
134 (name "r-diffusionmap")
139 (uri (cran-uri "diffusionMap" version))
142 "11l4kbciawvli5nlsi4qaf8afmgk5xgqiqpdyhvaqri5mx0zhk5j"))))
143 (properties `((upstream-name . "diffusionMap")))
144 (build-system r-build-system)
146 `(("r-igraph" ,r-igraph)
147 ("r-matrix" ,r-matrix)
148 ("r-scatterplot3d" ,r-scatterplot3d)))
149 (home-page "https://www.r-project.org")
150 (synopsis "Diffusion map")
151 (description "This package implements the diffusion map method of data
152 parametrization, including creation and visualization of diffusion maps,
153 clustering with diffusion K-means and regression using the adaptive regression
155 (license license:gpl2)))
157 (define-public r-rgraphviz
164 (uri (bioconductor-uri "Rgraphviz" version))
167 "0bp6517xsih0wng2rgkh9z4r1afqhwl3h04z6ssm7p4cdj0ahm4y"))))
168 (properties `((upstream-name . "Rgraphviz")))
169 (build-system r-build-system)
170 ;; FIXME: Rgraphviz bundles the sources of an older variant of
171 ;; graphviz. It does not build with the latest version of graphviz, so
172 ;; we do not add graphviz to the inputs.
173 (inputs `(("zlib" ,zlib)))
175 `(("r-graph" ,r-graph)))
177 `(("pkg-config" ,pkg-config)))
178 (home-page "http://bioconductor.org/packages/Rgraphviz")
179 (synopsis "Plotting capabilities for R graph objects")
181 "This package interfaces R with the graphviz library for plotting R graph
182 objects from the @code{graph} package.")
183 (license license:epl1.0)))
185 (define-public r-rbiofabric
186 (let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac")
189 (name "r-rbiofabric")
190 (version (string-append "0.3-" revision "." (string-take commit 7)))
194 (url "https://github.com/wjrl/RBioFabric.git")
196 (file-name (string-append name "-" version "-checkout"))
199 "1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z"))))
200 (build-system r-build-system)
202 `(("r-igraph" ,r-igraph)))
203 (home-page "http://www.biofabric.org/")
204 (synopsis "BioFabric network visualization")
205 (description "This package provides an implementation of the function
206 @code{bioFabric} for creating scalable network digrams where nodes are
207 represented by horizontal lines, and edges are represented by vertical
209 (license license:expat))))
211 (define-public python-plotly
213 (name "python-plotly")
218 (uri (pypi-uri "plotly" version))
221 "0s9gk2fl53x8wwncs3fwii1vzfngr0sskv15v3mpshqmrqfrk27m"))))
222 (build-system python-build-system)
224 '(#:tests? #f)) ; The tests are not distributed in the release
226 `(("python-decorator" ,python-decorator)
227 ("python-nbformat" ,python-nbformat)
228 ("python-pandas" ,python-pandas)
229 ("python-pytz" ,python-pytz)
230 ("python-requests" ,python-requests)
231 ("python-six" ,python-six)))
232 (home-page "https://plot.ly/python/")
233 (synopsis "Interactive plotting library for Python")
234 (description "Plotly's Python graphing library makes interactive,
235 publication-quality graphs online. Examples of how to make line plots, scatter
236 plots, area charts, bar charts, error bars, box plots, histograms, heatmaps,
237 subplots, multiple-axes, polar charts, and bubble charts. ")
238 (license license:expat)))
240 (define-public python2-plotly
241 (package-with-python2 python-plotly))