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
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
|
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages graph)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix packages)
#:use-module (guix build-system gnu)
#:use-module (guix build-system python)
#:use-module (guix build-system r)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gnu packages)
#:use-module (gnu packages gcc)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages compression)
#:use-module (gnu packages cran)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages maths)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages python-web)
#:use-module (gnu packages statistics)
#:use-module (gnu packages time)
#:use-module (gnu packages xml))
(define-public igraph
(package
(name "igraph")
(version "0.7.1")
(source
(origin
(method url-fetch)
(uri (string-append "http://igraph.org/nightly/get/c/igraph-"
version ".tar.gz"))
(sha256
(base32
"1pxh8sdlirgvbvsw8v65h6prn7hlm45bfsl1yfcgd6rn4w706y6r"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
(list "--with-external-glpk"
"--with-external-blas"
"--with-external-lapack")))
(inputs
`(("gmp" ,gmp)
("glpk" ,glpk)
("libxml2" ,libxml2)
("lapack" ,lapack)
("openblas" ,openblas)
("zlib" ,zlib)))
(home-page "http://igraph.org")
(synopsis "Network analysis and visualization")
(description
"This package provides a library for the analysis of networks and graphs.
It can handle large graphs very well and provides functions for generating
random and regular graphs, graph visualization, centrality methods and much
more.")
(license license:gpl2+)))
(define-public python-igraph
(package (inherit igraph)
(name "python-igraph")
(version "0.7.1.post6")
(source
(origin
(method url-fetch)
(uri (pypi-uri "python-igraph" version))
(sha256
(base32
"0xp61zz710qlzhmzbfr65d5flvsi8zf2xy78s6rsszh719wl5sm5"))))
(build-system python-build-system)
(arguments '())
(inputs
`(("igraph" ,igraph)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "http://pypi.python.org/pypi/python-igraph")
(synopsis "Python bindings for the igraph network analysis library")))
(define-public r-igraph
(package
(name "r-igraph")
(version "1.1.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "igraph" version))
(sha256
(base32
"1v26wyk52snh8z6m5p7yqwcd9dbqifhm57j112i9x53ppi0npcc9"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
(inputs
`(("gmp" ,gmp)
("libxml2" ,libxml2)))
(propagated-inputs
`(("r-irlba" ,r-irlba)
("r-magrittr" ,r-magrittr)
("r-matrix" ,r-matrix)
("r-pkgconfig" ,r-pkgconfig)))
(home-page "http://igraph.org")
(synopsis "Network analysis and visualization")
(description
"This package provides routines for simple graphs and network analysis.
It can handle large graphs very well and provides functions for generating
random and regular graphs, graph visualization, centrality methods and much
more.")
(license license:gpl2+)))
(define-public r-diffusionmap
(package
(name "r-diffusionmap")
(version "1.1-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "diffusionMap" version))
(sha256
(base32
"1l985q2hfc8ss5afajik4p25dx628yikvhdimz5s0pql800q2yv3"))))
(properties `((upstream-name . "diffusionMap")))
(build-system r-build-system)
(propagated-inputs
`(("r-igraph" ,r-igraph)
("r-matrix" ,r-matrix)
("r-scatterplot3d" ,r-scatterplot3d)))
(home-page "https://www.r-project.org")
(synopsis "Diffusion map")
(description "This package implements the diffusion map method of data
parametrization, including creation and visualization of diffusion maps,
clustering with diffusion K-means and regression using the adaptive regression
model.")
(license license:gpl2)))
(define-public r-rgraphviz
(package
(name "r-rgraphviz")
(version "2.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rgraphviz" version))
(sha256
(base32
"1y9nyjffa9644jch0p2i3w302fmnyc2kb0c3z1f3d5zp1p4qmyqv"))))
(properties `((upstream-name . "Rgraphviz")))
(build-system r-build-system)
;; FIXME: Rgraphviz bundles the sources of an older variant of
;; graphviz. It does not build with the latest version of graphviz, so
;; we do not add graphviz to the inputs.
(inputs `(("zlib" ,zlib)))
(propagated-inputs
`(("r-graph" ,r-graph)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "http://bioconductor.org/packages/Rgraphviz")
(synopsis "Plotting capabilities for R graph objects")
(description
"This package interfaces R with the graphviz library for plotting R graph
objects from the @code{graph} package.")
(license license:epl1.0)))
(define-public r-rbiofabric
(let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac")
(revision "1"))
(package
(name "r-rbiofabric")
(version (string-append "0.3-" revision "." (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/wjrl/RBioFabric.git")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z"))))
(build-system r-build-system)
(propagated-inputs
`(("r-igraph" ,r-igraph)))
(home-page "http://www.biofabric.org/")
(synopsis "BioFabric network visualization")
(description "This package provides an implementation of the function
@code{bioFabric} for creating scalable network digrams where nodes are
represented by horizontal lines, and edges are represented by vertical
lines.")
(license license:expat))))
(define-public python-plotly
(package
(name "python-plotly")
(version "2.4.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "plotly" version))
(sha256
(base32
"0s9gk2fl53x8wwncs3fwii1vzfngr0sskv15v3mpshqmrqfrk27m"))))
(build-system python-build-system)
(arguments
'(#:tests? #f)) ; The tests are not distributed in the release
(propagated-inputs
`(("python-decorator" ,python-decorator)
("python-nbformat" ,python-nbformat)
("python-pytz" ,python-pytz)
("python-requests" ,python-requests)
("python-six" ,python-six)))
(home-page "https://plot.ly/python/")
(synopsis "Interactive plotting library for Python")
(description "Plotly's Python graphing library makes interactive,
publication-quality graphs online. Examples of how to make line plots, scatter
plots, area charts, bar charts, error bars, box plots, histograms, heatmaps,
subplots, multiple-axes, polar charts, and bubble charts. ")
(license license:expat)))
(define-public python2-plotly
(package-with-python2 python-plotly))
|
