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Amine GHOZLANE
shaman
Commits
5072660c
Commit
5072660c
authored
Nov 22, 2016
by
Amine GHOZLANE
Browse files
Reactivate treeweight
parent
81a6528e
Changes
4
Hide whitespace changes
Inline
Side-by-side
LoadPackages.R
View file @
5072660c
options
(
download.file.method
=
'wget'
)
if
(
!
require
(
"Rcpp"
)){
install.packages
(
"Rcpp"
)
}
...
...
@@ -48,10 +50,10 @@ if (!require(devtools)) {
install.packages
(
'devtools'
)
library
(
devtools
)
}
#
if(!require(treeWeightD3)){
#
devtools::install_git
('https://gitlab.pasteur.fr/plechat
/treeWeightD3')
#
library(treeWeightD3)
#
}
if
(
!
require
(
treeWeightD3
)){
devtools
::
install_git
hub
(
'pierreLec
/treeWeightD3'
)
library
(
treeWeightD3
)
}
if
(
!
require
(
BiocInstaller
)){
source
(
"https://bioconductor.org/biocLite.R"
)
biocLite
(
"BiocInstaller"
)
...
...
Rfunctions/Data_Management.R
View file @
5072660c
...
...
@@ -380,6 +380,7 @@ GetCountsMerge <- function(input,dataInput,taxoSelect,target,design)
if
(
taxoSelect
==
"OTU/Gene"
)
counts
=
counts_annot
else
{
if
(
input
$
TypeTable
==
"MGS"
&&
input
$
FileFormat
!=
"fileBiom"
){
print
(
"MGS"
)
taxoS
=
taxo
[,
input
$
TypeTable
]
counts
=
aggregate
(
counts_annot
,
by
=
list
(
Taxonomy
=
taxoS
),
mean
)
rownames
(
counts
)
=
counts
[,
1
]
...
...
@@ -388,6 +389,7 @@ GetCountsMerge <- function(input,dataInput,taxoSelect,target,design)
rownames
(
counts_int
)
=
rownames
(
counts
)
colnames
(
counts_int
)
=
colnames
(
counts
)
counts
=
counts_int
print
(
"end"
)
}
if
(
taxoSelect
!=
"MGS"
||
input
$
FileFormat
==
"fileBiom"
){
#taxoS = taxo[ordOTU,taxoSelect]
...
...
server.R
View file @
5072660c
...
...
@@ -189,30 +189,25 @@ shinyServer(function(input, output,session) {
target
=
isolate
(
dataInputTarget
()
$
target
)
labeled
=
isolate
(
dataInputTarget
()
$
labeled
)
taxo
=
isolate
(
input
$
TaxoSelect
)
withProgress
(
if
(
!
is.null
(
data
$
counts
)
&&
!
is.null
(
data
$
taxo
)
&&
nrow
(
data
$
counts
)
>
0
&&
nrow
(
data
$
taxo
)
>
0
&&
!
is.null
(
taxo
)
&&
taxo
!=
"..."
&&
!
is.null
(
target
))
{
design
=
GetDesign
(
isolate
(
input
))
ChTM
=
CheckTargetModel
(
input
,
target
,
labeled
,
data
$
counts
)
$
Error
if
(
!
is.null
(
design
)
&&
is.null
(
ChTM
))
{
tmp
=
isolate
(
GetCountsMerge
(
input
,
data
,
taxo
,
target
,
design
))
counts
=
tmp
$
counts
## Filtering the counts
if
(
isolate
(
input
$
AddFilter
)
&&
!
is.null
(
isolate
(
input
$
SliderThSamp
))
&&
!
is.null
(
isolate
(
input
$
SliderThAb
)))
{
ind.filter
=
Filtered_feature
(
counts
,
isolate
(
input
$
SliderThSamp
),
isolate
(
input
$
SliderThAb
))
$
ind
counts
=
counts
[
-
ind.filter
,]
}
CheckTarget
=
tmp
$
CheckTarget
#target = tmp$target
#labeled = tmp$labeled
normFactors
=
tmp
$
normFactors
## OTU table, norm and no norm
CT_noNorm
=
tmp
$
CT_noNorm
CT_Norm
=
tmp
$
CT_Norm
...
...
@@ -1456,9 +1451,9 @@ shinyServer(function(input, output,session) {
filename
<-
function
()
{
paste
(
input
$
DiagPlot
,
paste
(
'SHAMAN'
,
input
$
Exp_format
,
sep
=
"."
),
sep
=
"_"
)
},
content
<-
function
(
file
)
{
if
(
input
$
Exp_format
==
"png"
)
png
(
file
,
width
=
input
$
widthDiagExport
,
height
=
input
$
heightDiagExport
)
if
(
input
$
Exp_format
==
"pdf"
)
pdf
(
file
,
width
=
input
$
widthDiagExport
/
96
,
height
=
input
$
heightDiagExport
/
96
)
if
(
input
$
Exp_format
==
"eps"
)
postscript
(
file
,
width
=
input
$
widthDiagExport
/
96
,
height
=
input
$
heightDiagExport
/
96
)
if
(
input
$
Exp_format
==
"svg"
)
svg
(
file
,
width
=
input
$
widthDiagExport
/
96
,
height
=
input
$
heightDiagExport
/
96
)
else
if
(
input
$
Exp_format
==
"pdf"
)
pdf
(
file
,
width
=
input
$
widthDiagExport
/
96
,
height
=
input
$
heightDiagExport
/
96
)
else
if
(
input
$
Exp_format
==
"eps"
)
postscript
(
file
,
width
=
input
$
widthDiagExport
/
96
,
height
=
input
$
heightDiagExport
/
96
)
else
if
(
input
$
Exp_format
==
"svg"
)
svg
(
file
,
width
=
input
$
widthDiagExport
/
96
,
height
=
input
$
heightDiagExport
/
96
)
print
(
Plot_diag
(
input
,
ResDiffAnal
()))
dev.off
()
...
...
@@ -1480,16 +1475,16 @@ shinyServer(function(input, output,session) {
taxo
=
input
$
TaxoSelect
if
(
input
$
Exp_format_Visu
==
"png"
)
png
(
file
,
width
=
input
$
widthVisuExport
,
height
=
input
$
heightVisuExport
)
if
(
input
$
Exp_format_Visu
==
"pdf"
)
pdf
(
file
,
width
=
input
$
widthVisuExport
/
96
,
height
=
input
$
heightVisuExport
/
96
)
if
(
input
$
Exp_format_Visu
==
"eps"
)
postscript
(
file
,
width
=
input
$
widthVisuExport
/
96
,
height
=
input
$
heightVisuExport
/
96
,
paper
=
"special"
)
if
(
input
$
Exp_format_Visu
==
"svg"
)
svg
(
file
,
width
=
input
$
widthVisuExport
/
96
,
height
=
input
$
heightVisuExport
/
96
)
else
if
(
input
$
Exp_format_Visu
==
"pdf"
)
pdf
(
file
,
width
=
input
$
widthVisuExport
/
96
,
height
=
input
$
heightVisuExport
/
96
)
else
if
(
input
$
Exp_format_Visu
==
"eps"
)
postscript
(
file
,
width
=
input
$
widthVisuExport
/
96
,
height
=
input
$
heightVisuExport
/
96
,
paper
=
"special"
)
else
if
(
input
$
Exp_format_Visu
==
"svg"
)
svg
(
file
,
width
=
input
$
widthVisuExport
/
96
,
height
=
input
$
heightVisuExport
/
96
)
if
(
input
$
PlotVisuSelect
==
"Barplot"
)
print
(
Plot_Visu_Barplot
(
input
,
ResDiffAnal
())
$
gg
)
if
(
input
$
PlotVisuSelect
==
"Heatmap"
)
Plot_Visu_Heatmap
(
input
,
ResDiffAnal
(),
export
=
TRUE
)
if
(
input
$
PlotVisuSelect
==
"Boxplot"
)
print
(
Plot_Visu_Boxplot
(
input
,
ResDiffAnal
(),
alpha
=
ifelse
(
input
$
Exp_format_Visu
==
"eps"
,
1
,
0.7
)))
if
(
input
$
PlotVisuSelect
==
"Scatterplot"
)
print
(
Plot_Visu_Scatterplot
(
input
,
ResDiffAnal
(),
export
=
TRUE
,
lmEst
=
FALSE
))
if
(
input
$
PlotVisuSelect
==
"Diversity"
)
print
(
Plot_Visu_Diversity
(
input
,
ResDiffAnal
())
$
plot
)
if
(
input
$
PlotVisuSelect
==
"Rarefaction"
)
print
(
Plot_Visu_Rarefaction
(
input
,
ResDiffAnal
(),
ranges
$
x
,
ranges
$
y
,
ylab
=
taxo
))
else
if
(
input
$
PlotVisuSelect
==
"Heatmap"
)
Plot_Visu_Heatmap
(
input
,
ResDiffAnal
(),
export
=
TRUE
)
else
if
(
input
$
PlotVisuSelect
==
"Boxplot"
)
print
(
Plot_Visu_Boxplot
(
input
,
ResDiffAnal
(),
alpha
=
ifelse
(
input
$
Exp_format_Visu
==
"eps"
,
1
,
0.7
)))
else
if
(
input
$
PlotVisuSelect
==
"Scatterplot"
)
print
(
Plot_Visu_Scatterplot
(
input
,
ResDiffAnal
(),
export
=
TRUE
,
lmEst
=
FALSE
))
else
if
(
input
$
PlotVisuSelect
==
"Diversity"
)
print
(
Plot_Visu_Diversity
(
input
,
ResDiffAnal
())
$
plot
)
else
if
(
input
$
PlotVisuSelect
==
"Rarefaction"
)
print
(
Plot_Visu_Rarefaction
(
input
,
ResDiffAnal
(),
ranges
$
x
,
ranges
$
y
,
ylab
=
taxo
))
dev.off
()
}
...
...
@@ -1505,9 +1500,9 @@ shinyServer(function(input, output,session) {
taxo
=
input
$
TaxoSelect
if
(
input
$
Exp_format_VisuComp
==
"png"
)
png
(
file
,
width
=
input
$
widthVisuExportComp
,
height
=
input
$
heightVisuExportComp
)
if
(
input
$
Exp_format_VisuComp
==
"pdf"
)
pdf
(
file
,
width
=
input
$
widthVisuExportComp
/
96
,
height
=
input
$
heightVisuExportComp
/
96
)
if
(
input
$
Exp_format_VisuComp
==
"eps"
)
postscript
(
file
,
width
=
input
$
widthVisuExportComp
/
96
,
height
=
input
$
heightVisuExportComp
/
96
,
paper
=
"special"
)
if
(
input
$
Exp_format_VisuComp
==
"svg"
)
svg
(
file
,
width
=
input
$
widthVisuExportComp
/
96
,
height
=
input
$
heightVisuExportComp
/
96
)
else
if
(
input
$
Exp_format_VisuComp
==
"pdf"
)
pdf
(
file
,
width
=
input
$
widthVisuExportComp
/
96
,
height
=
input
$
heightVisuExportComp
/
96
)
else
if
(
input
$
Exp_format_VisuComp
==
"eps"
)
postscript
(
file
,
width
=
input
$
widthVisuExportComp
/
96
,
height
=
input
$
heightVisuExportComp
/
96
,
paper
=
"special"
)
else
if
(
input
$
Exp_format_VisuComp
==
"svg"
)
svg
(
file
,
width
=
input
$
widthVisuExportComp
/
96
,
height
=
input
$
heightVisuExportComp
/
96
)
BaseContrast
=
read.table
(
namesfile
,
header
=
TRUE
)
filesize
=
file.info
(
namesfile
)[,
"size"
]
...
...
@@ -1708,16 +1703,16 @@ shinyServer(function(input, output,session) {
##
#####################################################
#
output$PlotVisuTree <- renderTreeWeightD3({
#
resDiff = ResDiffAnal()
#
taxo_table = dataInput()$data$taxo
#
CT_Norm_OTU = dataMergeCounts()$CT_Norm
#
res = NULL
#
if(!is.null(resDiff$dds) && length(input$VisuVarInt)>=1) res = Plot_Visu_Tree(input,resDiff,CT_Norm_OTU,taxo_table)
#
return(res)
#
#
})
#
output
$
PlotVisuTree
<-
renderTreeWeightD3
({
resDiff
=
ResDiffAnal
()
taxo_table
=
dataInput
()
$
data
$
taxo
CT_Norm_OTU
=
dataMergeCounts
()
$
CT_Norm
res
=
NULL
if
(
!
is.null
(
resDiff
$
dds
)
&&
length
(
input
$
VisuVarInt
)
>=
1
)
res
=
Plot_Visu_Tree
(
input
,
resDiff
,
CT_Norm_OTU
,
taxo_table
)
return
(
res
)
})
output
$
PlotVisuBar
<-
renderChart
({
resDiff
=
ResDiffAnal
()
...
...
@@ -1909,7 +1904,7 @@ shinyServer(function(input, output,session) {
if
(
input
$
PlotVisuSelect
==
"Barplot"
)
res
=
showOutput
(
"PlotVisuBar"
)
if
(
input
$
PlotVisuSelect
==
"Heatmap"
)
res
=
d3heatmapOutput
(
"heatmap"
,
height
=
input
$
heightVisu
+10
)
if
(
input
$
PlotVisuSelect
==
"Boxplot"
)
res
=
plotOutput
(
"Boxplot"
,
height
=
input
$
heightVisu
+10
)
#
if(input$PlotVisuSelect=="Tree") res = treeWeightD3Output('PlotVisuTree', height = input$heightVisu+10,width="100%")
if
(
input
$
PlotVisuSelect
==
"Tree"
)
res
=
treeWeightD3Output
(
'PlotVisuTree'
,
height
=
input
$
heightVisu
+10
,
width
=
"100%"
)
if
(
input
$
PlotVisuSelect
==
"Scatterplot"
&&
!
input
$
AddRegScatter
)
res
=
scatterD3Output
(
"ScatterplotD3"
,
height
=
input
$
heightVisu
+10
)
if
(
input
$
PlotVisuSelect
==
"Scatterplot"
&&
input
$
AddRegScatter
)
res
=
plotOutput
(
"Scatterplotgg"
,
height
=
input
$
heightVisu
+10
)
...
...
@@ -2160,28 +2155,28 @@ shinyServer(function(input, output,session) {
})
#
output$VarIntVisuTree <- renderUI({
#
#
target=dataInputTarget()$target
#
data = dataInput()$data
#
taxo = input$TaxoSelect
#
resDiff = ResDiffAnal()
#
res = NULL
#
#
if(!is.null(data$counts) && !is.null(data$taxo) && nrow(data$counts)>0 && nrow(data$taxo)>0 && !is.null(taxo) && taxo!="..." && !is.null(target))
#
{
#
counts = dataMergeCounts()$counts
#
#
Available_x = sort(rownames(counts))
#
#
res = selectizeInput("TaxoTree",h6(strong(paste("Select a specific",taxo,sep=" "))),c("...",Available_x),multiple = FALSE)
#
#
}
#
#
return(res)
#
#
})
#
output
$
VarIntVisuTree
<-
renderUI
({
target
=
dataInputTarget
()
$
target
data
=
dataInput
()
$
data
taxo
=
input
$
TaxoSelect
resDiff
=
ResDiffAnal
()
res
=
NULL
if
(
!
is.null
(
data
$
counts
)
&&
!
is.null
(
data
$
taxo
)
&&
nrow
(
data
$
counts
)
>
0
&&
nrow
(
data
$
taxo
)
>
0
&&
!
is.null
(
taxo
)
&&
taxo
!=
"..."
&&
!
is.null
(
target
))
{
counts
=
dataMergeCounts
()
$
counts
Available_x
=
sort
(
rownames
(
counts
))
res
=
selectizeInput
(
"TaxoTree"
,
h6
(
strong
(
paste
(
"Select a specific"
,
taxo
,
sep
=
" "
))),
c
(
"..."
,
Available_x
),
multiple
=
FALSE
)
}
return
(
res
)
})
#####################################################
##
## KRONA
...
...
ui.R
View file @
5072660c
...
...
@@ -5,10 +5,10 @@ if (!require(devtools)) {
install.packages
(
'devtools'
)
library
(
devtools
)
}
#
if(!require(treeWeightD3)){
#
devtools::install_git
('https://gitlab.pasteur.fr/plechat
/treeWeightD3
.git
')
#
library(treeWeightD3)
#
}
if
(
!
require
(
treeWeightD3
)){
devtools
::
install_git
hub
(
'pierreLec
/treeWeightD3'
)
library
(
treeWeightD3
)
}
if
(
!
require
(
scatterD3
))
{
devtools
::
install_github
(
'aghozlane/scatterD3'
)
library
(
scatterD3
)
...
...
@@ -606,8 +606,8 @@ body <- dashboardBody(
column
(
width
=
3
,
box
(
title
=
"Select your plot"
,
width
=
NULL
,
status
=
"primary"
,
solidHeader
=
TRUE
,
collapsible
=
FALSE
,
collapsed
=
FALSE
,
#
selectizeInput("PlotVisuSelect","",c("Barplot"="Barplot","Heatmap"="Heatmap","Boxplot"="Boxplot","Tree"="Tree","Scatterplot"="Scatterplot","Diversity"="Diversity","Rarefaction"="Rarefaction"),selected = "
Tree
")
selectizeInput
(
"PlotVisuSelect"
,
""
,
c
(
"Barplot"
=
"Barplot"
,
"Heatmap"
=
"Heatmap"
,
"Boxplot"
=
"Boxplot"
,
"Scatterplot"
=
"Scatterplot"
,
"Diversity"
=
"Diversity"
,
"Rarefaction"
=
"Rarefaction"
),
selected
=
"Barplot"
)
selectizeInput
(
"PlotVisuSelect"
,
""
,
c
(
"Barplot"
=
"Barplot"
,
"Heatmap"
=
"Heatmap"
,
"Boxplot"
=
"Boxplot"
,
"Tree"
=
"Tree"
,
"Scatterplot"
=
"Scatterplot"
,
"Diversity"
=
"Diversity"
,
"Rarefaction"
=
"Rarefaction"
),
selected
=
"
Barplot
"
)
#
selectizeInput("PlotVisuSelect","",c("Barplot"="Barplot","Heatmap"="Heatmap","Boxplot"="Boxplot","Scatterplot"="Scatterplot","Diversity"="Diversity","Rarefaction"="Rarefaction"),selected = "Barplot")
),
...
...
@@ -622,8 +622,8 @@ body <- dashboardBody(
h5
(
strong
(
"Select the modalities"
)),
uiOutput
(
"ModVisu"
)
),
#
conditionalPanel(condition="input.PlotVisuSelect=='Tree' ",
#
uiOutput("VarIntVisuTree")),
conditionalPanel
(
condition
=
"input.PlotVisuSelect=='Tree' "
,
uiOutput
(
"VarIntVisuTree"
)),
conditionalPanel
(
condition
=
"input.PlotVisuSelect=='Scatterplot' "
,
uiOutput
(
"VarIntVisuScatter"
),
radioButtons
(
"TransDataScatter"
,
"Data transformation"
,
c
(
"Log2 +1"
=
"log2"
,
"None"
=
"none"
),
inline
=
TRUE
),
...
...
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