Supported by Dr. Osamu Ogasawara and  providing  . |
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Last data update: 2014.03.03 |
Makes a GO graph highlighting the GO terms in the selected cell of the results table.Description
Usage
graphCell(object, row, col = 1, set, ontology = "BP", interact = TRUE,
legend.pos = "bottomleft", print.legend = TRUE,
use.col="red", bg.col = "grey80")
Arguments
DetailsTo access the tutorial document for this package, type in R: ValueInvisibly returns Author(s)John R. Stevens and Dennis S. Mecham ReferencesStevens, J. R., and Isom, S. C., 2012. "Gene set testing to characterize multivariately differentially expressed genes." Conference on Applied Statistics in Agriculture Proceedings, 24, pp. 125-137. Mecham, D. S. (2014) "mvGST: Multivariate and Directional Gene Set Testing". MS Project, Utah State University, Department of Mathematics and Statistics. http://digitalcommons.usu.edu/gradreports/382/ Examples
data(mvGSTsamples)
# object obatoclax.mvGST returned by profileTable
obatoclax.mvGST
# plots a GO Graph highlighting the GO ID's from the cell
# in the fifth row and first column (the column for
# cell line RS4) of the results.table of the object
# returned by profileTable
graphCell(obatoclax.mvGST, 5, 1, ontology = "BP", interact = FALSE)
# See package vignette for larger examples with discussion:
# vignette("mvGST")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(mvGST)
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: Rgraphviz
Loading required package: graph
Loading required package: grid
Attaching package: 'Rgraphviz'
The following objects are masked from 'package:IRanges':
from, to
The following objects are masked from 'package:S4Vectors':
from, to
Attaching package: 'mvGST'
The following object is masked from 'package:base':
cut
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mvGST/graphCell.Rd_%03d_medium.png", width=480, height=480)
> ### Name: graphCell
> ### Title: Makes a GO graph highlighting the GO terms in the selected cell
> ### of the results table.
> ### Aliases: graphCell
>
> ### ** Examples
>
> data(mvGSTsamples)
> # object obatoclax.mvGST returned by profileTable
> obatoclax.mvGST
Low High RS4 SEMK2
0 0 11711 11157
0 1 16 707
1 1 285 397
1 0 403 116
0 -1 56 156
-1 -1 87 55
-1 0 40 10
>
> # plots a GO Graph highlighting the GO ID's from the cell
> # in the fifth row and first column (the column for
> # cell line RS4) of the results.table of the object
> # returned by profileTable
> graphCell(obatoclax.mvGST, 5, 1, ontology = "BP", interact = FALSE)
Terms
1 regulation of alternative mRNA splicing, via spliceosome
2 alternative mRNA splicing, via spliceosome
3 regulation of mRNA splicing, via spliceosome
4 IMP biosynthetic process
5 rRNA transcription
6 mRNA splicing, via spliceosome
7 activation of signaling protein activity involved in unfolded protein response
8 ER-associated ubiquitin-dependent protein catabolic process
9 purine ribonucleoside monophosphate biosynthetic process
10 purine ribonucleoside monophosphate catabolic process
11 IMP metabolic process
12 purine ribonucleotide biosynthetic process
13 ncRNA transcription
14 RNA splicing, via transesterification reactions with bulged adenosine as nucleophile
15 positive regulation of protein kinase activity
16 proteasome-mediated ubiquitin-dependent protein catabolic process
17 regulation of gluconeogenesis involved in cellular glucose homeostasis
18 posttranslational protein targeting to membrane, translocation
19 mevalonate transport
20 purine nucleoside monophosphate biosynthetic process
21 ribonucleoside monophosphate biosynthetic process
22 purine ribonucleoside monophosphate metabolic process
23 purine nucleoside monophosphate catabolic process
24 ribonucleoside monophosphate catabolic process
25 purine ribonucleotide metabolic process
26 purine nucleotide biosynthetic process
27 ribonucleotide biosynthetic process
28 ncRNA metabolic process
29 RNA splicing, via transesterification reactions
30 positive regulation of protein phosphorylation
31 transcription, DNA-templated
32 regulation of protein kinase activity
33 positive regulation of kinase activity
34 regulation of mRNA processing
35 ubiquitin-dependent protein catabolic process
36 posttranscriptional regulation of gene expression
37 regulation of RNA splicing
38 protein N-linked glycosylation via asparagine
39 branched-chain amino acid metabolic process
40 regulation of gluconeogenesis
41 posttranslational protein targeting to membrane
42 monocarboxylic acid transport
43 long-chain fatty-acyl-CoA biosynthetic process
44 nucleoside monophosphate biosynthetic process
45 purine nucleoside monophosphate metabolic process
46 ribonucleoside monophosphate metabolic process
47 nucleoside monophosphate catabolic process
48 purine nucleotide metabolic process
49 ribonucleotide metabolic process
50 nucleotide biosynthetic process
51 positive regulation of phosphorylation
52 nucleic acid-templated transcription
53 mRNA processing
54 RNA splicing
55 regulation of protein phosphorylation
56 regulation of kinase activity
57 regulation of mRNA metabolic process
58 modification-dependent protein catabolic process
59 positive regulation of protein modification process
60 regulation of gene expression
61 peptidyl-asparagine modification
62 proteasomal protein catabolic process
63 protein N-linked glycosylation
64 cellular amino acid metabolic process
65 regulation of glucose metabolic process
66 gluconeogenesis
67 positive regulation of transferase activity
68 protein targeting to membrane
69 protein targeting to ER
70 protein export from nucleus
71 carboxylic acid transport
72 endoplasmic reticulum unfolded protein response
73 long-chain fatty-acyl-CoA metabolic process
74 fatty-acyl-CoA biosynthetic process
75 nucleoside monophosphate metabolic process
76 nucleotide metabolic process
77 nucleoside phosphate biosynthetic process
78 regulation of phosphorylation
79 positive regulation of phosphate metabolic process
80 nucleoside phosphate catabolic process
81 ribose phosphate biosynthetic process
82 RNA biosynthetic process
83 mRNA metabolic process
84 RNA processing
85 protein phosphorylation
86 modification-dependent macromolecule catabolic process
87 reelin-mediated signaling pathway
88 regulation of protein modification process
89 peptidyl-amino acid modification
90 proteolysis involved in cellular protein catabolic process
91 protein glycosylation
92 carboxylic acid metabolic process
93 positive regulation of cellular protein metabolic process
94 regulation of RNA metabolic process
95 positive regulation of nuclease activity
96 glucose metabolic process
97 hexose biosynthetic process
98 regulation of transferase activity
99 cellular glucose homeostasis
100 protein localization to T-tubule
101 establishment of protein localization to endoplasmic reticulum
102 intracellular protein transmembrane transport
103 protein targeting
104 nuclear export
105 organic anion transport
106 cellular response to unfolded protein
107 fatty-acyl-CoA metabolic process
108 acyl-CoA biosynthetic process
109 nucleoside phosphate metabolic process
110 phosphorylation
111 ribose phosphate metabolic process
112 regulation of phosphate metabolic process
113 organophosphate catabolic process
114 organophosphate biosynthetic process
115 positive regulation of phosphorus metabolic process
116 RNA metabolic process
117 gene expression
118 cell surface receptor signaling pathway
119 glycoprotein biosynthetic process
120 cellular protein modification process
121 cellular protein catabolic process
122 ERAD pathway
123 proteolysis
124 oxoacid metabolic process
125 regulation of cellular protein metabolic process
126 macromolecule glycosylation
127 positive regulation of nucleobase-containing compound metabolic process
128 positive regulation of protein metabolic process
129 regulation of cellular carbohydrate metabolic process
130 regulation of nuclease activity
131 regulation of carbohydrate biosynthetic process
132 hexose metabolic process
133 monosaccharide biosynthetic process
134 positive regulation of hydrolase activity
135 voluntary musculoskeletal movement
136 glucose homeostasis
137 protein localization to plasma membrane
138 establishment of protein localization to membrane
139 protein localization to endoplasmic reticulum
140 establishment of protein localization to organelle
141 protein transmembrane transport
142 intracellular protein transport
143 single-organism intracellular transport
144 anion transport
145 nucleocytoplasmic transport
146 response to unfolded protein
147 cellular response to topologically incorrect protein
148 response to endoplasmic reticulum stress
149 acyl-CoA metabolic process
150 coenzyme biosynthetic process
151 thioester biosynthetic process
152 phosphate-containing compound metabolic process
153 organophosphate metabolic process
154 nucleobase-containing compound catabolic process
155 nucleobase-containing compound biosynthetic process
156 regulation of phosphorus metabolic process
157 purine-containing compound biosynthetic process
158 nucleic acid metabolic process
159 cellular macromolecule catabolic process
160 signal transduction
161 cellular macromolecule biosynthetic process
162 glycoprotein metabolic process
163 macromolecule methylation
164 nucleobase-containing small molecule metabolic process
165 carbohydrate derivative biosynthetic process
166 protein modification process
167 cellular protein metabolic process
168 protein catabolic process
169 single-organism catabolic process
170 organic acid metabolic process
171 positive regulation of cellular metabolic process
172 regulation of protein metabolic process
173 regulation of nucleobase-containing compound metabolic process
174 positive regulation of macromolecule metabolic process
175 positive regulation of nitrogen compound metabolic process
176 glycosylation
177 regulation of carbohydrate metabolic process
178 carbohydrate biosynthetic process
179 monosaccharide metabolic process
180 small molecule biosynthetic process
181 regulation of hydrolase activity
182 positive regulation of catalytic activity
183 plasma membrane organization
184 cellular chemical homeostasis
185 musculoskeletal movement
186 positive regulation of binding
187 carbohydrate homeostasis
188 protein localization to membrane
189 protein localization to cell periphery
190 protein localization to organelle
191 transmembrane transport
192 protein transport
193 ion transport
194 organic acid transport
195 organic hydroxy compound transport
196 cytoplasmic transport
197 nuclear transport
198 response to topologically incorrect protein
199 cellular response to organic substance
200 cellular response to stress
201 coenzyme metabolic process
202 thioester metabolic process
203 phosphorus metabolic process
204 cofactor biosynthetic process
205 sulfur compound biosynthetic process
206 aromatic compound catabolic process
207 heterocycle catabolic process
208 cellular nitrogen compound catabolic process
209 aromatic compound biosynthetic process
210 heterocycle biosynthetic process
211 cellular nitrogen compound biosynthetic process
212 purine-containing compound metabolic process
213 nucleobase-containing compound metabolic process
214 carbohydrate derivative metabolic process
215 cellular macromolecule metabolic process
216 organic cyclic compound catabolic process
217 organic cyclic compound biosynthetic process
218 macromolecule catabolic process
219 macromolecule biosynthetic process
220 macromolecule modification
221 organonitrogen compound biosynthetic process
222 cell communication
223 protein metabolic process
224 cellular carbohydrate metabolic process
225 regulation of cellular metabolic process
226 positive regulation of cellular process
227 regulation of macromolecule metabolic process
228 regulation of nitrogen compound metabolic process
229 regulation of primary metabolic process
230 positive regulation of metabolic process
231 single-organism carbohydrate metabolic process
232 regulation of biosynthetic process
233 small molecule metabolic process
234 single-organism biosynthetic process
235 regulation of catalytic activity
236 single-organism membrane organization
237 cellular homeostasis
238 multicellular organismal movement
239 positive regulation of molecular function
240 regulation of binding
241 chemical homeostasis
242 single-organism cellular localization
243 cellular protein localization
244 establishment of protein localization
245 single-organism transport
246 organic substance transport
247 intracellular transport
248 response to stress
249 response to organic substance
250 cellular response to chemical stimulus
251 cofactor metabolic process
252 sulfur compound metabolic process
253 cellular catabolic process
254 cellular biosynthetic process
255 cellular aromatic compound metabolic process
256 heterocycle metabolic process
257 cellular nitrogen compound metabolic process
258 single organism signaling
259 organic cyclic compound metabolic process
260 organic substance catabolic process
261 macromolecule metabolic process
262 organonitrogen compound metabolic process
263 organic substance biosynthetic process
264 regulation of cellular process
265 single-organism cellular process
266 carbohydrate metabolic process
267 positive regulation of biological process
268 regulation of metabolic process
269 single-organism metabolic process
270 membrane organization
271 endomembrane system organization
272 single-multicellular organism process
273 regulation of molecular function
274 homeostatic process
275 single-organism localization
276 cellular macromolecule localization
277 protein localization
278 transport
279 establishment of localization in cell
280 response to chemical
281 cellular response to stimulus
282 cellular metabolic process
283 catabolic process
284 organic substance metabolic process
285 methylation
286 nitrogen compound metabolic process
287 biosynthetic process
288 primary metabolic process
289 regulation of biological process
290 single-organism process
291 cellular component organization
292 regulation of biological quality
293 cellular localization
294 macromolecule localization
295 establishment of localization
296 response to stimulus
297 signaling
298 cellular process
299 metabolic process
300
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Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and