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Bagueneau Mathias
Shiny SChnurR
Commits
dbe03eca
Commit
dbe03eca
authored
Apr 25, 2019
by
Bagueneau Mathias
Browse files
- Test Readme
- Seconde miniature Compare
parent
30dd3652
Changes
2
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README.md
View file @
dbe03eca
# Titre 1
-
Liste
-
Liste
-
Liste
# Shiny SChnurR
## Sous-titre 1

```
code```
Ou bien `code en ligne`
**Table of Contents**
Et *emphasize* ou _comme ça_
[TOC]
# Installation
Hello
# Tutorial
Hello
## Visualisation Page
Hey !
## HeatMap Page
Hello
## Genes Page
Hello
## Compare Page
Hello
## Pipeline Page
Hello
----
app.R
View file @
dbe03eca
...
...
@@ -194,7 +194,7 @@ body <- dashboardBody(
uiOutput
(
outputId
=
"clusters_infos_compare"
),
br
(),
conditionalPanel
(
condition
=
"output.fileUploaded"
,
fluidRow
(
column
(
align
=
"center"
,
width
=
2
,
plotOutput
(
outputId
=
"miniplot_compare"
,
width
=
"250px"
,
height
=
"250px"
)),
fluidRow
(
column
(
align
=
"center"
,
width
=
2
,
plotOutput
(
outputId
=
"miniplot_compare"
,
width
=
"250px"
,
height
=
"250px"
),
br
(),
plotOutput
(
outputId
=
"miniplot_compare2"
,
width
=
"250px"
,
height
=
"250px"
)),
column
(
align
=
"center"
,
width
=
5
,
plotlyOutput
(
"plot1_compare"
,
width
=
"450px"
,
height
=
"450px"
),
br
(),
uiOutput
(
"plot1_library"
),
downloadButton
(
"dl_compare1"
,
label
=
""
)),
column
(
align
=
"center"
,
width
=
5
,
plotlyOutput
(
"plot2_compare"
,
width
=
"450px"
,
height
=
"450px"
),
br
(),
uiOutput
(
"plot2_library"
),
downloadButton
(
"dl_compare2"
,
label
=
""
))
),
...
...
@@ -289,9 +289,11 @@ server <- function(input, output, session) {
miniplot_compareData
<-
reactive
({
if
(
input
$
choice_compare
==
"f_compare"
)
{
withProgress
(
DimPlot
(
object
=
filedata
$
data
,
label
=
TRUE
,
pt.size
=
input
$
ptsize_compare
,
legend
=
"none"
,
reduction
=
input
$
graph_compare
,
group.by
=
input
$
fsel2
),
message
=
"Plot Generation"
,
value
=
1
)
+
theme_bw
()
+
NoAxes
()
+
NoLegend
()
}
else
{
})
miniplot_compare2Data
<-
reactive
({
if
(
input
$
choice_compare
==
"features_compare"
)
{
if
(
input
$
featuresel2
==
"d2"
)
{
withProgress
(
FeaturePlot
(
object
=
filedata
$
data
,
cols
=
c
(
"lightgrey"
,
plasma
(
ceiling
(
max
(
eval
(
parse
(
text
=
paste0
(
"filedata$data@meta.data$"
,
input
$
nsel2
))))))),
pt.size
=
input
$
ptsize_compare
,
features
=
input
$
nsel2
,
reduction
=
input
$
graph_compare
),
message
=
"Plot Generation"
,
value
=
1
)
+
theme_bw
()
+
NoAxes
()
}
else
if
(
input
$
featuresel2
==
"g2"
)
{
...
...
@@ -301,7 +303,6 @@ server <- function(input, output, session) {
})
plot1_compareData
<-
reactive
({
# df.colors <- data.frame(class=unique(eval(parse(text=paste0("filedata$data@meta.data$",input$fsel2)))), color="viridis"(length(unique(eval(parse(text=paste0("filedata$data@meta.data$",input$fsel2)))))))
scalex
<-
scale_x_continuous
(
limits
=
c
(
min
(
filedata
$
data
@
reductions
[[
input
$
graph_compare
]]
@
cell.embeddings
[,
1
]),
max
(
filedata
$
data
@
reductions
[[
input
$
graph_compare
]]
@
cell.embeddings
[,
1
])))
scaley
<-
scale_y_continuous
(
limits
=
c
(
min
(
filedata
$
data
@
reductions
[[
input
$
graph_compare
]]
@
cell.embeddings
[,
1
]),
max
(
filedata
$
data
@
reductions
[[
input
$
graph_compare
]]
@
cell.embeddings
[,
1
])))
cells_to_plot
<-
rownames
(
filedata
$
data
@
meta.data
)[
which
(
eval
(
parse
(
text
=
paste0
(
"filedata$data@meta.data$"
,
input
$
fsel2
)))
%in%
input
$
library1_compare
)]
...
...
@@ -354,6 +355,11 @@ server <- function(input, output, session) {
req
(
filedata
$
data
)
plot
(
miniplot_compareData
())
})
output
$
miniplot_compare2
<-
renderPlot
({
req
(
filedata
$
data
)
plot
(
miniplot_compare2Data
())
})
output
$
plot1_compare
<-
renderPlotly
({
req
(
filedata
$
data
)
...
...
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