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Amine GHOZLANE
shaman
Commits
62b15d53
Commit
62b15d53
authored
Aug 27, 2019
by
Amine GHOZLANE
Browse files
Add modification of taxonomical table
parent
c798d6c2
Pipeline
#13998
passed with stage
in 46 minutes and 49 seconds
Changes
2
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
server.R
View file @
62b15d53
...
...
@@ -13,6 +13,7 @@ shinyServer(function(input, output,session) {
namesfile
=
tempfile
(
pattern
=
"BaseContrast"
,
tmpdir
=
tempdir
(),
fileext
=
""
)
file.create
(
namesfile
,
showWarnings
=
FALSE
)
target
=
NULL
taxo
=
NULL
## JSON name for masque
curdir
=
getwd
()
...
...
@@ -25,7 +26,7 @@ shinyServer(function(input, output,session) {
observe
(
if
(
input
$
AddRegScatter
)
info
(
"By adding the regression line, you will lose interactivity."
))
## Reactive target
values
<-
reactiveValues
(
TargetWorking
=
target
,
labeled
=
NULL
,
fastq_names_only
=
NULL
,
R1fastQ
=
NULL
,
R2fastQ
=
NULL
,
values
<-
reactiveValues
(
TargetWorking
=
target
,
TaxoWorking
=
taxo
,
labeled
=
NULL
,
fastq_names_only
=
NULL
,
R1fastQ
=
NULL
,
R2fastQ
=
NULL
,
json_name
=
json_name
,
num
=
0
,
pass
=
pass
,
login_email
=
NULL
,
is.valid
=
NULL
,
biom_masque
=
NULL
,
tree_masque
=
NULL
,
masque_key
=
NULL
,
count_table_masque
=
NULL
,
rdp_annot_masque
=
NULL
,
rdp_thres_masque
=
NULL
,
...
...
@@ -68,9 +69,8 @@ shinyServer(function(input, output,session) {
## Taxo File
dataInputTaxo
<-
reactive
({
inFile
<-
input
$
fileTaxo
values
$
TaxoWorking
=
NULL
if
(
is.null
(
inFile
)
&&
is.null
(
values
$
rdp_annot_masque
))
return
(
NULL
)
#if (is.null(inFile)) return(NULL)
...
...
@@ -260,15 +260,14 @@ shinyServer(function(input, output,session) {
data
=
NULL
check
=
NULL
percent
=
NULL
Taxo
=
NULL
Taxo
=
values
$
TaxoWorking
Counts
=
NULL
inputData
=
NULL
target
=
NULL
if
(
input
$
FileFormat
==
"fileCounts"
)
{
Counts
=
dataInputCounts
()
if
(
!
input
$
NoTaxoFile
)
Taxo
=
dataInputTaxo
()
if
(
!
input
$
NoTaxoFile
&&
is.null
(
Taxo
)
)
Taxo
=
dataInputTaxo
()
if
(
!
is.null
(
Counts
)
&&
input
$
NoTaxoFile
)
{
Taxo
=
data.frame
(
rownames
(
Counts
),
row.names
=
rownames
(
Counts
));
names
(
Taxo
)
=
NA
}
if
(
!
is.null
(
Counts
)
&&
!
is.null
(
Taxo
))
...
...
@@ -280,21 +279,30 @@ shinyServer(function(input, output,session) {
check
=
list
(
CheckCounts
=
tmp
$
CheckCounts
,
CheckTaxo
=
tmp
$
CheckTaxo
,
CheckPercent
=
tmp
$
CheckPercent
)
percent
=
tmp
$
Percent
}
}
}
if
(
input
$
FileFormat
==
"fileBiom"
)
{
tmpBIOM
=
dataInputBiom
()
if
(
!
is.null
(
tmpBIOM
))
if
(
!
is.null
(
tmpBIOM
)
&&
is.null
(
data
)
)
{
tmp
=
GetDataFromBIOM
(
tmpBIOM
)
data
=
list
(
counts
=
tmp
$
counts
,
taxo
=
tmp
$
taxo
,
target
=
tmp
$
target
,
taxo_biom
=
tmp
$
taxo_biom
)
if
(
!
is.null
(
Taxo
)){
data
=
list
(
counts
=
tmp
$
counts
,
taxo
=
Taxo
,
target
=
tmp
$
target
,
taxo_biom
=
tmp
$
taxo_biom
)
tmp_check
=
CheckTaxoTable
(
Taxo
,
tmp
$
counts
)
tmp_annot
=
PercentAnnot
(
tmp
$
counts
,
Taxo
)
check
=
list
(
CheckCounts
=
tmp_check
$
CheckCounts
,
CheckTaxo
=
tmp_check
$
CheckTaxo
,
Percent
=
tmp_annot
$
Percent
,
CheckPercent
=
tmp_annot
$
Error
)
percent
=
tmp_annot
$
Percent
}
else
{
data
=
list
(
counts
=
tmp
$
counts
,
taxo
=
tmp
$
taxo
,
target
=
tmp
$
target
,
taxo_biom
=
tmp
$
taxo_biom
)
## Remove row with only O
# data[["counts"]] = data[["counts"]][rowSums(data[["counts"]])>1,]
check
=
list
(
CheckCounts
=
tmp
$
CheckCounts
,
CheckTaxo
=
tmp
$
CheckTaxo
,
CheckPercent
=
tmp
$
CheckPercent
)
percent
=
tmp
$
Percent
check
=
list
(
CheckCounts
=
tmp
$
CheckCounts
,
CheckTaxo
=
tmp
$
CheckTaxo
,
CheckPercent
=
tmp
$
CheckPercent
)
percent
=
tmp
$
Percent
}
#if(!is.null(data$target)) values$TargetWorking = data$target
}
}
...
...
@@ -452,9 +460,10 @@ shinyServer(function(input, output,session) {
# Infobox Error counts
output
$
valueErrorPercent
<-
renderInfoBox
({
tmp
=
dataInput
()
{
values
$
TaxoWorking
tmp
=
dataInput
()
}
data
=
tmp
$
data
if
(
!
is.null
(
values
$
TaxoWorking
))
tmp
=
dataInput
()
check
=
tmp
$
check
cond
=
(
!
is.null
(
data
$
counts
)
&&
nrow
(
data
$
counts
)
>
0
&&
!
is.null
(
data
$
taxo
)
&&
nrow
(
data
$
taxo
)
>
0
)
res
=
shinydashboardshaman
::
valueBox
(
paste0
(
0
,
"%"
),
h6
(
strong
(
"Annotated features"
)),
color
=
"light-blue"
,
width
=
NULL
,
icon
=
icon
(
"list"
))
...
...
@@ -613,11 +622,26 @@ shinyServer(function(input, output,session) {
## Taxonomy table
output
$
DataTaxo
<-
DT
::
renderDataTable
(
dataInput
()
$
data
$
taxo
,
editable
=
T
,
options
=
list
(
lengthMenu
=
list
(
c
(
10
,
50
,
-1
),
c
(
'10'
,
'50'
,
'All'
)),
pageLength
=
10
,
scrollX
=
TRUE
,
processing
=
FALSE
))
pageLength
=
10
,
scrollX
=
TRUE
,
processing
=
FALSE
)
)
# "table.on('click', '#DataTaxo button', function () {
# Shiny.onInputChange('lastClickId',this.id);
# Shiny.onInputChange('lastClick', Math.random())
# );")
proxy
=
dataTableProxy
(
'DataTaxo'
)
observeEvent
(
input
$
DataTaxo_cell_edit
,
{
info
=
input
$
DataTaxo_cell_edit
str
(
info
)
i
=
info
$
row
j
=
info
$
col
v
=
info
$
value
tmp
=
as.matrix
(
dataInput
()
$
data
$
taxo
)
tmp
[
i
,
j
]
=
v
values
$
TaxoWorking
=
as.data.frame
(
tmp
)
replaceData
(
proxy
,
values
$
TaxoWorking
,
resetPaging
=
FALSE
)
})
## Tab box for data visualisation
output
$
TabBoxData
<-
renderUI
({
tree
=
dataInputTree
()
$
data
...
...
@@ -627,22 +651,25 @@ shinyServer(function(input, output,session) {
{
res
=
tabBox
(
width
=
NULL
,
selected
=
"Count table"
,
tabPanel
(
"Count table"
,
DT
::
dataTableOutput
(
"DataCounts"
)),
tabPanel
(
"Taxonomy"
,
DT
::
dataTableOutput
(
"DataTaxo"
)),
tabPanel
(
"Taxonomy"
,
DT
::
dataTableOutput
(
"DataTaxo"
),
actionButton
(
"deleteTax"
,
"Delete annotation"
),
downloadButton
(
'ExportTaxo'
,
'Export taxonomy file'
)),
tabPanel
(
"Summary"
,
h5
(
strong
(
"Percentage of annotation"
)),
htmlOutput
(
"SummaryView"
),
br
(),
h5
(
strong
(
"Number of features by level:"
)),
plotOutput
(
"SummaryViewBarplot"
,
width
=
1200
,
height
=
500
)),
tabPanel
(
"Phylogeny"
,
PhyloTreeMetaROutput
(
'PhyloTreeMetaR'
))
)
}
else
if
(
is.null
(
tree
))
else
{
res
=
tabBox
(
width
=
NULL
,
selected
=
"Count table"
,
tabPanel
(
"Count table"
,
DT
::
dataTableOutput
(
"DataCounts"
)),
tabPanel
(
"Taxonomy"
,
DT
::
dataTableOutput
(
"DataTaxo"
)),
tabPanel
(
"Taxonomy"
,
DT
::
dataTableOutput
(
"DataTaxo"
),
actionButton
(
"deleteTax"
,
"Delete annotation"
),
downloadButton
(
'ExportTaxo'
,
'Export taxonomy file'
)),
tabPanel
(
"Summary"
,
h5
(
strong
(
"Percentage of annotation"
)),
htmlOutput
(
"SummaryView"
),
br
(),
h5
(
strong
(
"Number of features by level:"
)),
plotOutput
(
"SummaryViewBarplot"
,
width
=
1200
,
height
=
500
))
)
}
return
(
res
)
})
...
...
@@ -1978,7 +2005,15 @@ shinyServer(function(input, output,session) {
######################## END MASQUE #################################
observeEvent
(
input
$
deleteTax
,{
if
(
is.null
(
values
$
TaxoWorking
))
values
$
TaxoWorking
=
dataInput
()
$
data
$
taxo
if
(
!
is.null
(
input
$
DataTaxo_rows_selected
))
{
if
(
nrow
(
values
$
TaxoWorking
)
!=
0
)
values
$
labeled
<-
(
nrow
(
values
$
TaxoWorking
)
-
length
(
input
$
DataTaxo_rows_selected
))
*
values
$
labeled
/
nrow
(
values
$
TaxoWorking
)
else
values
$
labeled
<-
0
values
$
TaxoWorking
<-
values
$
TaxoWorking
[
-
as.numeric
(
input
$
DataTaxo_rows_selected
),]
}
})
observeEvent
(
input
$
deleteRows
,{
...
...
ui.R
View file @
62b15d53
...
...
@@ -593,7 +593,11 @@ function(request) {
),
column
(
id
=
"tabboxdata_col"
,
width
=
12
,
uiOutput
(
"TabBoxData"
))
#,
column
(
id
=
"tabboxdata_col"
,
width
=
12
,
uiOutput
(
"TabBoxData"
)),
tags
$
script
(
"$(document).on('click', '#DataTaxo button', function () {
Shiny.onInputChange('lastClickId',this.id);
Shiny.onInputChange('lastClick', Math.random())
);"
)
# receiveSweetAlert(messageId = "ErrorTaxo"),
# receiveSweetAlert(messageId = "ErrorBiom1"),
# receiveSweetAlert(messageId = "ErrorBiom2"),
...
...
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