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Amine GHOZLANE
shaman
Commits
cdddde0a
Commit
cdddde0a
authored
Aug 08, 2019
by
Perrine Woringer
Browse files
Debug clustering and pca, plus some cometics
parent
8c8b8e19
Changes
3
Hide whitespace changes
Inline
Side-by-side
LoadPackages.R
View file @
cdddde0a
...
...
@@ -66,11 +66,11 @@ if(!require(treeWeightD3)){
devtools
::
install_github
(
'pierreLec/treeWeightD3'
)
library
(
treeWeightD3
)
}
if
(
!
require
(
BiocInstaller
)){
source
(
"https://bioconductor.org/biocLite.R"
)
biocLite
(
"BiocInstaller"
)
library
(
BiocInstaller
)
}
#
if (!require(BiocInstaller)){
#
source("https://bioconductor.org/biocLite.R")
#
biocLite("BiocInstaller")
#
library(BiocInstaller)
#
}
if
(
!
require
(
d3heatmap
))
{
devtools
::
install_github
(
'aghozlane/d3heatmap'
)
...
...
@@ -263,3 +263,8 @@ if(!require("visNetwork")){
install.packages
(
"visNetwork"
)
library
(
visNetwork
)
}
if
(
!
require
(
"SummarizedExperiment"
)){
BiocManager
::
install
(
"SummarizedExperiment"
)
library
(
SummarizedExperiment
)
}
\ No newline at end of file
Rfunctions/DiagPlot.R
View file @
cdddde0a
...
...
@@ -138,7 +138,7 @@ HCPlot <- function (input,dds,group,type.trans=NULL,counts=NULL,CT,tree,col = c(
## Get the type of dendrogram
type
<-
input
$
typeHculst
dend
<-
set
(
dend
,
"labels_cex"
,
input
$
cexLabelDiag
)
#
dend <- set(dend, "labels_cex", input$cexLabelDiag)
if
(
input
$
colorHC
)
labels_colors
(
dend
)
<-
col
[
as.integer
(
as.factor
(
group
))][
order.dendrogram
(
dend
)]
if
(
type
==
"hori"
)
{
...
...
@@ -148,7 +148,8 @@ HCPlot <- function (input,dds,group,type.trans=NULL,counts=NULL,CT,tree,col = c(
else
{
par
(
cex
=
input
$
cexTitleDiag
,
mar
=
c
(
6
,
6
,
4
,
5
))
res
=
circlize_dendrogram
(
dend
,
labels_track_height
=
0.2
,
dend_track_height
=
.3
,
main
=
"Cluster dendrogram"
,
xlab
=
paste
(
input
$
DistClust
,
"distance, Ward criterion"
,
sep
=
" "
))
res
=
circlize_dendrogram
(
dend
,
labels_track_height
=
0.2
,
dend_track_height
=
.3
,
main
=
"Cluster dendrogram"
,
xlab
=
paste
(
input
$
DistClust
,
"distance, Ward criterion"
,
sep
=
" "
),
labels_cex
=
input
$
cexLabelDiag
)
}
}
}
...
...
@@ -554,8 +555,8 @@ PCAPlot_meta <-function(input,dds, group_init, n = min(500, nrow(counts(dds))),
{
type.trans
<-
type.trans
[
1
]
if
(
type.trans
==
"VST"
)
counts.trans
<-
assay
(
varianceStabilizingTransformation
(
dds
))
else
counts.trans
<-
assay
(
rlogTransformation
(
dds
))
if
(
type.trans
==
"VST"
)
counts.trans
<-
SummarizedExperiment
::
assay
(
varianceStabilizingTransformation
(
dds
))
else
counts.trans
<-
SummarizedExperiment
::
assay
(
rlogTransformation
(
dds
))
counts.trans
=
counts.trans
[,
ind_kept
]
rv
=
apply
(
counts.trans
,
1
,
var
,
na.rm
=
TRUE
)
...
...
@@ -754,8 +755,8 @@ Get_pca_table <-function(input,dds, group_init, n = min(500, nrow(counts(dds))),
{
type.trans
<-
type.trans
[
1
]
if
(
type.trans
==
"VST"
)
counts.trans
<-
assay
(
varianceStabilizingTransformation
(
dds
))
else
counts.trans
<-
assay
(
rlogTransformation
(
dds
))
if
(
type.trans
==
"VST"
)
counts.trans
<-
SummarizedExperiment
::
assay
(
varianceStabilizingTransformation
(
dds
))
else
counts.trans
<-
SummarizedExperiment
::
assay
(
rlogTransformation
(
dds
))
counts.trans
=
counts.trans
[,
ind_kept
]
rv
=
apply
(
counts.trans
,
1
,
var
,
na.rm
=
TRUE
)
...
...
ui.R
View file @
cdddde0a
...
...
@@ -1234,7 +1234,7 @@ function(request) {
),
column
(
width
=
3
,
box
(
title
=
"Select your plot"
,
width
=
NULL
,
status
=
"primary"
,
solidHeader
=
TRUE
,
collapsible
=
FALSE
,
collapsed
=
FALSE
,
selectizeInput
(
"PlotVisuSelectComp"
,
""
,
c
(
"Venn diagram"
=
"Venn"
,
"Heatmap"
=
"Heatmap_comp"
,
"Logit plot"
=
"LogitPlot"
,
"
p value d
ensity"
=
"pValueDensity"
,
"UpSet"
=
"UpSet"
,
"Multiple venn compair"
=
"multipleVenn"
),
selected
=
"Heatmap_comp"
)
selectizeInput
(
"PlotVisuSelectComp"
,
""
,
c
(
"Venn diagram"
=
"Venn"
,
"UpSet"
=
"UpSet"
,
"Contrasts compair"
=
"multipleVenn"
,
"Heatmap"
=
"Heatmap_comp"
,
"Logit plot"
=
"LogitPlot"
,
"
D
ensity
plot
"
=
"pValueDensity"
),
selected
=
"Heatmap_comp"
)
),
box
(
title
=
"Options"
,
width
=
NULL
,
status
=
"primary"
,
solidHeader
=
TRUE
,
collapsible
=
TRUE
,
collapsed
=
FALSE
,
conditionalPanel
(
condition
=
"input.PlotVisuSelectComp=='Heatmap_comp' || input.PlotVisuSelectComp=='UpSet' || input.PlotVisuSelectComp=='pValueDensity' || input.PlotVisuSelectComp=='multipleVenn'"
,
...
...
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