LoadPackages.R 3.37 KB
Newer Older
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
1
2
options(download.file.method = 'wget')

svolant's avatar
svolant committed
3
4
5
if (!require("Rcpp")){
  install.packages("Rcpp")
}
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
6
7
8
9
if(!require(shiny)){
  install.packages("shiny")
  library(shiny)
}
svolant's avatar
svolant committed
10
if(!require(shinydashboard)){
svolant's avatar
svolant committed
11
  devtools::install_github('aghozlane/shinydashboard')
svolant's avatar
svolant committed
12
13
14
15
16
  library(shinydashboard)
}

if(!require(rjson)){
  install.packages('rjson')
svolant's avatar
svolant committed
17
18
19
20
21
22
23
24
25
26
  library(rjson)
}
if(!require(ape)){
  install.packages('ape')
  library(ape)
}

if(!require(GUniFrac)){
  install.packages('GUniFrac')
  library(GUniFrac)
svolant's avatar
svolant committed
27
28
29
30
}

if(!require(devtools)){
  install.packages('devtools')
svolant's avatar
svolant committed
31
  library(devtools)
svolant's avatar
svolant committed
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
}

if (!require(psych)) {
  install.packages('psych')
  library(psych)
}

if (!require(ggplot2)) {
  install.packages('ggplot2')
  library(ggplot2)
}

if (!require(vegan)) {
  install.packages('vegan')
  library(vegan)
}

if (!require(dendextend)) {
  install.packages('dendextend')
  library(dendextend)
}

if (!require(circlize)) {
  install.packages('circlize')
  library(circlize)
}


if (!require(devtools)) {
  install.packages('devtools')
  library(devtools)
}
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
64
65
66
67
if(!require(treeWeightD3)){
   devtools::install_github('pierreLec/treeWeightD3')
   library(treeWeightD3)
}
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
68
69
70
71
72
if (!require(BiocInstaller)){
  source("https://bioconductor.org/biocLite.R")
  biocLite("BiocInstaller")
  library(BiocInstaller)
}
svolant's avatar
svolant committed
73

74
75
76
77
78
if (!require(d3heatmap)) {
  devtools::install_github('aghozlane/d3heatmap')
  library(d3heatmap)
}

79
80
# Let us use biomformat instead of biom
if (!require(biomformat)){
81
 devtools::install_github("aghozlane/biomformat")
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
82
library(biomformat)
83
84
}

svolant's avatar
svolant committed
85
if (!require(scatterD3)) {
86
  devtools::install_github('aghozlane/scatterD3')
svolant's avatar
svolant committed
87
88
89
90
  library(scatterD3)
}

if (!require(rNVD3)) {
91
  devtools::install_github('aghozlane/rNVD3')
svolant's avatar
svolant committed
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
  library(rNVD3)
}

if (!require(genefilter)) {
  source("https://bioconductor.org/biocLite.R")
  biocLite("genefilter")
  library(genefilter)
}

if (!require(googleVis)) {
  install.packages('googleVis')
  suppressPackageStartupMessages(library(googleVis))
}

if (!require(shinyjs)) {
  install.packages('shinyjs')
  library(shinyjs)
}

if(!require(d3vennR)){
  install_github("timelyportfolio/d3vennR")
  library(d3vennR)
}

if (!require(DT)) {
  install.packages('DT')
  library(DT)
}

if (!require(RColorBrewer)) {
  install.packages('RColorBrewer')
  library(RColorBrewer)
}

if (!require(gplots)) {
  install.packages('gplots')
  library(gplots)
}

if (!require(DESeq2)) {
  source("https://bioconductor.org/biocLite.R")
  biocLite("DESeq2")
  library(DESeq2)
}

if (!require(ade4)) {
  install.packages('ade4')
  library(ade4)
}

if (!require(scales)) {
  install.packages('scales')
  library(scales)
}
svolant's avatar
svolant committed
146
147
148
149
150
151

if (!require(phytools)) {
  install.packages('phytools')
  library(phytools)
}

152
153
154
155
if(!require(philentropy)){
  devtools::install_github("HajkD/philentropy", build_vignettes = TRUE, dependencies = TRUE)
  library(philentropy)
}
svolant's avatar
svolant committed
156

157
158
159
160
161
if(!require(PhyloTreeMetaR)){
  devtools::install_github("https://github.com/pierreLec/PhyloTreeMetaR.git")
  library(PhyloTreeMetaR)
}

162
163
164
165
# if(!require(plotly)){
#   install.packages("plotly")
#   library(plotly)  
# }
svolant's avatar
svolant committed
166

167
168
169
170
171
172
173
# Allow to upload 50M files only shaman server
if(Sys.info()["nodename"] == "shaman"){
  options(shiny.maxRequestSize=50*1024^2)
}else{
  # No limit
  options(shiny.maxRequestSize=500000000000000*1024^2)
}
svolant's avatar
svolant committed
174
175
176
177
178
179
180
181
source("Rfunctions/Data_Management.R")
source("Rfunctions/Stat_Model.R")
source("Rfunctions/DiagPlot.R")
source("Rfunctions/VisuPlot.R")
source("Rfunctions/CompPlot.R")
source("Rfunctions/DiffTable.R")