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Amine GHOZLANE
shaman
Commits
1a379492
Commit
1a379492
authored
Oct 05, 2016
by
Amine GHOZLANE
Browse files
Remove useless save and clean DT call
parent
30e7ed5a
Changes
8
Hide whitespace changes
Inline
Side-by-side
.gitignore
View file @
1a379492
...
...
@@ -2,3 +2,4 @@
*.Rhistory
*.RData
.Rproj.user
*.Rproj
META16S_App.Rproj
deleted
100644 → 0
View file @
30e7ed5a
Version: 1.0
RestoreWorkspace: Default
SaveWorkspace: Default
AlwaysSaveHistory: Default
EnableCodeIndexing: Yes
UseSpacesForTab: Yes
NumSpacesForTab: 2
Encoding: UTF-8
RnwWeave: Sweave
LaTeX: pdfLaTeX
Rfunctions/CompPlot.R
View file @
1a379492
...
...
@@ -252,6 +252,7 @@ GetData_venn <-function(input,SelContrast,BaseContrast,resDiff)
}
}
print
(
df.tot
)
return
(
list
(
res
=
res
,
df.tot
=
df.tot
))
}
Rfunctions/Data_Management.R
View file @
1a379492
...
...
@@ -195,7 +195,7 @@ GetCountsMerge <- function(input,dataInput,taxoSelect,target,design)
CT
=
CT_int
}
else
CT
=
CT
[,
ind
]
save.image
(
"test.RData"
)
#
save.image("test.RData")
## Order CT according to the target
CT
=
OrderCounts
(
counts
=
CT
,
labels
=
labels
)
$
CountsOrder
CT_noNorm
=
CT
...
...
@@ -240,7 +240,7 @@ GetCountsMerge <- function(input,dataInput,taxoSelect,target,design)
## Keep normalized OTU table
CT_Norm
=
counts
(
dds
,
normalized
=
TRUE
)
save
(
CT_Norm
,
dds
,
CT
,
taxo
,
taxoSelect
,
file
=
"test.RData"
)
#
save(CT_Norm,dds,CT,taxo,taxoSelect,file="test.RData")
# Only interesting OTU
# merged_table = merge(CT, taxo[order(rownames(CT)),], by="row.names")
merged_table
=
merge
(
CT
,
taxo
,
by
=
"row.names"
)
...
...
Rfunctions/Stat_Model.R
View file @
1a379492
...
...
@@ -43,7 +43,7 @@ Get_dds_object <- function(input,counts,target,design,normFactorsOTU,CT_noNorm,C
}
countsNorm
=
counts
(
dds
,
normalized
=
TRUE
)
save
(
dds
,
file
=
"dds.RData"
)
#
save(dds,file="dds.RData")
return
(
list
(
dds
=
dds
,
raw_counts
=
counts
,
countsNorm
=
countsNorm
,
target
=
target
,
design
=
design
,
normFactors
=
normFactorsOTU
,
CT_noNorm
=
CT_noNorm
,
CT_Norm
=
CT_Norm
))
}
...
...
Rfunctions/VisuPlot.R
View file @
1a379492
...
...
@@ -413,6 +413,7 @@ Plot_Visu_Diversity <- function(input,resDiff,ForScatter=FALSE){
## Get interactivity
#ff = ggplotly(gg)
}
print
(
dataTmp
)
return
(
list
(
plot
=
gg
,
dataDiv
=
dataTmp
))
}
...
...
server.R
View file @
1a379492
source
(
'LoadPackages.R'
)
renderDataTable
<-
DT
::
renderDataTable
dataTableOutput
<-
DT
::
dataTableOutput
shinyServer
(
function
(
input
,
output
,
session
)
{
...
...
@@ -308,25 +305,26 @@ shinyServer(function(input, output,session) {
#####################################################
## Counts Table
output
$
DataCounts
<-
renderDataTable
(
output
$
DataCounts
<-
DT
::
renderDataTable
(
dataInput
()
$
data
$
counts
,
options
=
list
(
lengthMenu
=
list
(
c
(
10
,
50
,
-1
),
c
(
'10'
,
'50'
,
'All'
)),
pageLength
=
10
,
scrollX
=
TRUE
,
processing
=
FALSE
))
## Counts Table
output
$
DataVenn
<-
renderDataTable
({
SelContrast
=
input
$
ContrastList_table_FC
resDiff
=
ResDiffAnal
()
BaseContrast
=
read.table
(
namesfile
,
header
=
TRUE
)
GetData_venn
(
input
,
SelContrast
,
BaseContrast
,
resDiff
)
$
df.tot
},
options
=
list
(
lengthMenu
=
list
(
c
(
10
,
50
,
-1
),
c
(
'10'
,
'50'
,
'All'
)),
output
$
DataVenn
<-
DT
::
renderDataTable
(
#{
#SelContrast = input$ContrastList_table_FC
#resDiff = ResDiffAnal()
#BaseContrast = read.table(namesfile,header=TRUE)
GetData_venn
(
input
,
input
$
ContrastList_table_FC
,
read.table
(
namesfile
,
header
=
TRUE
),
ResDiffAnal
())
$
df.tot
,
#}
options
=
list
(
lengthMenu
=
list
(
c
(
10
,
50
,
-1
),
c
(
'10'
,
'50'
,
'All'
)),
pageLength
=
10
,
scrollX
=
TRUE
,
processing
=
FALSE
))
## Taxonomy table
output
$
DataTaxo
<-
renderDataTable
(
output
$
DataTaxo
<-
DT
::
renderDataTable
(
dataInput
()
$
data
$
taxo
,
options
=
list
(
lengthMenu
=
list
(
c
(
10
,
50
,
-1
),
c
(
'10'
,
'50'
,
'All'
)),
pageLength
=
10
,
scrollX
=
TRUE
,
processing
=
FALSE
...
...
@@ -341,8 +339,8 @@ shinyServer(function(input, output,session) {
if
(
!
is.null
(
data
$
counts
)
&&
!
is.null
(
data
$
taxo
)
&&
nrow
(
data
$
counts
)
>
0
&&
nrow
(
data
$
taxo
)
>
0
)
{
tabBox
(
width
=
NULL
,
selected
=
"Count table"
,
tabPanel
(
"Count table"
,
dataTableOutput
(
"DataCounts"
)),
tabPanel
(
"Taxonomy"
,
dataTableOutput
(
"DataTaxo"
)),
tabPanel
(
"Count table"
,
DT
::
dataTableOutput
(
"DataCounts"
)),
tabPanel
(
"Taxonomy"
,
DT
::
dataTableOutput
(
"DataTaxo"
)),
tabPanel
(
"Summary"
,
h5
(
strong
(
"Percentage of annotation"
)),
htmlOutput
(
"SummaryView"
),
br
(),
h5
(
strong
(
"Number of features by level:"
)),
plotOutput
(
"SummaryViewBarplot"
,
width
=
1200
,
height
=
500
))
)
...
...
@@ -531,14 +529,14 @@ shinyServer(function(input, output,session) {
## target table
output
$
DataTarget
<-
renderDataTable
(
output
$
DataTarget
<-
DT
::
renderDataTable
(
dataInputTarget
()
$
target
,
options
=
list
(
lengthMenu
=
list
(
c
(
10
,
50
,
-1
),
c
(
'10'
,
'50'
,
'All'
)),
pageLength
=
10
,
scrollX
=
TRUE
,
processing
=
FALSE
))
## Counts table for the selected taxonomy level
output
$
CountsMerge
<-
renderDataTable
(
output
$
CountsMerge
<-
DT
::
renderDataTable
(
round
(
counts
(
ResDiffAnal
()
$
dds
,
normalized
=
TRUE
)),
options
=
list
(
lengthMenu
=
list
(
c
(
10
,
50
,
-1
),
c
(
'10'
,
'50'
,
'All'
)),
pageLength
=
10
,
scrollX
=
TRUE
,
processing
=
FALSE
...
...
@@ -554,7 +552,7 @@ shinyServer(function(input, output,session) {
if
(
!
is.null
(
counts
)
&&
taxo
!=
"..."
)
{
box
(
title
=
paste
(
"Count table ("
,
taxo
,
")"
,
sep
=
""
),
width
=
NULL
,
status
=
"primary"
,
solidHeader
=
TRUE
,
collapsible
=
TRUE
,
collapsed
=
TRUE
,
dataTableOutput
(
"CountsMerge"
),
DT
::
dataTableOutput
(
"CountsMerge"
),
downloadButton
(
'ExportCounts'
,
'Export normalised counts'
),
downloadButton
(
'ExportRelative'
,
'Export relative abundance'
)
)
...
...
@@ -589,7 +587,7 @@ shinyServer(function(input, output,session) {
if
(
!
is.null
(
target
)
&&
nrow
(
target
)
>
0
)
{
box
(
title
=
"Target file overview"
,
width
=
NULL
,
status
=
"primary"
,
solidHeader
=
TRUE
,
collapsible
=
TRUE
,
collapsed
=
TRUE
,
dataTableOutput
(
"DataTarget"
)
DT
::
dataTableOutput
(
"DataTarget"
)
)
}
...
...
@@ -1145,7 +1143,7 @@ shinyServer(function(input, output,session) {
})
output
$
SizeFactTable
<-
renderDataTable
(
output
$
SizeFactTable
<-
DT
::
renderDataTable
(
SizeFactor_table
(),
options
=
list
(
scrollX
=
TRUE
,
searching
=
FALSE
,
processing
=
FALSE
))
...
...
@@ -1338,27 +1336,27 @@ shinyServer(function(input, output,session) {
})
## Significant diff table
output
$
DataDiffsignificant
<-
renderDataTable
(
output
$
DataDiffsignificant
<-
DT
::
renderDataTable
(
datatable
(
dataDiff
()
$
significant
,
rownames
=
FALSE
),
options
=
list
(
lengthMenu
=
list
(
c
(
10
,
50
,
-1
),
c
(
'10'
,
'50'
,
'All'
)),
pageLength
=
10
,
scrollX
=
TRUE
,
processing
=
FALSE
))
## Complete diff table
output
$
DataDiffcomplete
<-
renderDataTable
(
output
$
DataDiffcomplete
<-
DT
::
renderDataTable
(
datatable
(
dataDiff
()
$
complete
,
rownames
=
FALSE
),
options
=
list
(
lengthMenu
=
list
(
c
(
10
,
50
,
-1
),
c
(
'10'
,
'50'
,
'All'
)),
pageLength
=
10
,
scrollX
=
TRUE
,
processing
=
FALSE
))
## Up diff table
output
$
DataDiffup
<-
renderDataTable
(
output
$
DataDiffup
<-
DT
::
renderDataTable
(
datatable
(
dataDiff
()
$
up
,
rownames
=
FALSE
),
options
=
list
(
lengthMenu
=
list
(
c
(
10
,
50
,
-1
),
c
(
'10'
,
'50'
,
'All'
)),
pageLength
=
10
,
scrollX
=
TRUE
,
processing
=
FALSE
))
## Down diff table
output
$
DataDiffdown
<-
renderDataTable
(
output
$
DataDiffdown
<-
DT
::
renderDataTable
(
datatable
(
dataDiff
()
$
down
,
rownames
=
FALSE
),
options
=
list
(
lengthMenu
=
list
(
c
(
10
,
50
,
-1
),
c
(
'10'
,
'50'
,
'All'
)),
pageLength
=
10
,
scrollX
=
TRUE
,
processing
=
FALSE
...
...
@@ -1374,10 +1372,10 @@ shinyServer(function(input, output,session) {
{
tabBox
(
width
=
NULL
,
selected
=
"Significant"
,
tabPanel
(
"Significant"
,
dataTableOutput
(
"DataDiffsignificant"
)),
tabPanel
(
"Complete"
,
dataTableOutput
(
"DataDiffcomplete"
)),
tabPanel
(
"Up"
,
dataTableOutput
(
"DataDiffup"
)),
tabPanel
(
"Down"
,
dataTableOutput
(
"DataDiffdown"
))
tabPanel
(
"Significant"
,
DT
::
dataTableOutput
(
"DataDiffsignificant"
)),
tabPanel
(
"Complete"
,
DT
::
dataTableOutput
(
"DataDiffcomplete"
)),
tabPanel
(
"Up"
,
DT
::
dataTableOutput
(
"DataDiffup"
)),
tabPanel
(
"Down"
,
DT
::
dataTableOutput
(
"DataDiffdown"
))
)
}
...
...
@@ -1512,14 +1510,14 @@ shinyServer(function(input, output,session) {
## Regression coefficients Table
output
$
lmRegScatter
<-
renderDataTable
(
output
$
lmRegScatter
<-
DT
::
renderDataTable
(
Plot_Visu_Scatterplot
(
input
,
ResDiffAnal
(),
lmEst
=
TRUE
)
$
regCoef
,
options
=
list
(
lengthMenu
=
list
(
c
(
10
,
50
,
-1
),
c
(
'10'
,
'50'
,
'All'
)),
pageLength
=
10
,
scrollX
=
TRUE
,
processing
=
FALSE
))
## Correlation coefficients Table
output
$
CorTable
<-
renderDataTable
(
output
$
CorTable
<-
DT
::
renderDataTable
(
Plot_Visu_Scatterplot
(
input
,
ResDiffAnal
(),
CorEst
=
TRUE
)
$
cor.est
,
options
=
list
(
lengthMenu
=
list
(
c
(
10
,
50
,
-1
),
c
(
'10'
,
'50'
,
'All'
)),
pageLength
=
10
,
scrollX
=
TRUE
,
processing
=
FALSE
...
...
@@ -1562,12 +1560,12 @@ shinyServer(function(input, output,session) {
})
output
$
Diversitytable
<-
renderDataTable
({
output
$
Diversitytable
<-
DT
::
renderDataTable
(
datatable
({
resDiff
=
ResDiffAnal
()
tmp
=
Plot_Visu_Diversity
(
input
,
resDiff
)
$
dataDiv
tmp
$
VarX
=
NULL
;
tmp
$
VarCol
=
NULL
datatable
(
tmp
[,
c
(
4
,
5
,
1
,
2
,
3
)],
rownames
=
FALSE
)
},
tmp
[,
c
(
4
,
5
,
1
,
2
,
3
)]},
rownames
=
FALSE
),
options
=
list
(
lengthMenu
=
list
(
c
(
10
,
50
,
-1
),
c
(
'10'
,
'50'
,
'All'
)),
pageLength
=
10
,
scrollX
=
TRUE
,
processing
=
FALSE
))
...
...
ui.R
View file @
1a379492
...
...
@@ -370,7 +370,7 @@ body <- dashboardBody(
br
(),
conditionalPanel
(
condition
=
"input.DiagPlot=='SfactorsVStot'"
,
box
(
title
=
"Size factors"
,
width
=
NULL
,
status
=
"primary"
,
solidHeader
=
TRUE
,
collapsible
=
TRUE
,
collapsed
=
TRUE
,
dataTableOutput
(
"SizeFactTable"
),
DT
::
dataTableOutput
(
"SizeFactTable"
),
fluidRow
(
column
(
width
=
3
,
downloadButton
(
'ExportSizeFactor'
,
'Export table'
)),
column
(
width
=
3
,
selectInput
(
"sepsizef"
,
h6
(
strong
(
"Separator:"
)),
c
(
"Tab"
=
"\t"
,
"Comma"
=
","
,
"Semicolon"
=
";"
)))
...
...
@@ -517,7 +517,7 @@ body <- dashboardBody(
column
(
width
=
6
,
br
(),
box
(
title
=
"Regression coefficients"
,
width
=
NULL
,
status
=
"primary"
,
solidHeader
=
TRUE
,
collapsible
=
TRUE
,
collapsed
=
TRUE
,
dataTableOutput
(
"lmRegScatter"
)
DT
::
dataTableOutput
(
"lmRegScatter"
)
)
),
column
(
width
=
6
,
br
(),
htmlOutput
(
"lmEquation"
))
...
...
@@ -528,7 +528,7 @@ body <- dashboardBody(
br
(),
p
(
actionButton
(
"scatterD3-reset-zoom"
,
HTML
(
"<span class='glyphicon glyphicon-search' aria-hidden='true'></span> Reset Zoom"
)),
Align
=
"right"
),
box
(
title
=
"Correlation table"
,
width
=
NULL
,
status
=
"primary"
,
solidHeader
=
TRUE
,
collapsible
=
TRUE
,
collapsed
=
TRUE
,
dataTableOutput
(
"CorTable"
)
DT
::
dataTableOutput
(
"CorTable"
)
)
),
...
...
@@ -536,7 +536,7 @@ body <- dashboardBody(
conditionalPanel
(
condition
=
"input.PlotVisuSelect=='Diversity'"
,
br
(),
box
(
title
=
"Diversity values"
,
width
=
NULL
,
status
=
"primary"
,
solidHeader
=
TRUE
,
collapsible
=
TRUE
,
collapsed
=
TRUE
,
dataTableOutput
(
"Diversitytable"
),
DT
::
dataTableOutput
(
"Diversitytable"
),
fluidRow
(
column
(
width
=
3
,
downloadButton
(
'ExportDiversitytable'
,
'Export table'
)),
column
(
width
=
3
,
selectInput
(
"sepdiversity"
,
"Separator:"
,
c
(
"Tab"
=
"\t"
,
"Comma"
=
","
,
"Semicolon"
=
";"
)))
...
...
@@ -699,7 +699,7 @@ body <- dashboardBody(
column
(
width
=
9
,
uiOutput
(
"plotVisuComp"
),
conditionalPanel
(
condition
=
"input.PlotVisuSelectComp=='Venn'"
,
dataTableOutput
(
"DataVenn"
)
DT
::
dataTableOutput
(
"DataVenn"
)
)
),
column
(
width
=
3
,
...
...
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