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Cedric Midoux
Easy16S
Commits
41ab68de
Commit
41ab68de
authored
Mar 30, 2021
by
Cedric Midoux
Browse files
DeseqResults
parent
d62ef33f
Changes
1
Hide whitespace changes
Inline
Side-by-side
panels/deseq-server.R
View file @
41ab68de
...
...
@@ -38,16 +38,6 @@ output$deseqTitleUI <- renderUI({
value
=
"Volcano Plot"
)
})
output
$
deseqPadjUI
<-
renderUI
({
validate
(
need
(
physeq
(),
""
))
sliderInput
(
"deseqPadj"
,
label
=
"Adjusted p-value threshold (recommended 0.05 ):"
,
min
=
0
,
max
=
1
,
value
=
0.05
,
step
=
0.01
)
})
output
$
deseqUI
<-
renderUI
({
validate
(
need
(
physeq
(),
""
))
box
(
...
...
@@ -56,27 +46,42 @@ output$deseqUI <- renderUI({
status
=
"primary"
,
uiOutput
(
"deseqContrastVarUI"
),
uiOutput
(
"deseqContrastModUI"
),
uiOutput
(
"deseqTitleUI
"
),
uiOutput
(
"deseq
Padj
UI"
)
# actionButton("deseqButton", label = "Execute", icon = icon("check"), class = "btn-primary
"),
uiOutput
(
"deseq
Title
UI"
)
)
})
output
$
deseq
<-
metaRender2
(
renderPlot
,
{
validate
(
need
(
physeq
(),
"Requires an abundance dataset"
),
need
(
class
(
get_variable
(
physeq
(),
input
$
deseqContrastVar
))
!=
"numeric"
||
length
(
input
$
deseqContrastMod
)
==
2
,
"Requires a continuous design or a selection of two modalities for a discrete design."
)
)
design
<-
metaReactive2
({
req
(
input
$
deseqContrastVar
)
metaExpr
({
as.formula
(
..
(
paste
(
"~"
,
input
$
deseqContrastVar
)))})
})
cds
<-
metaReactive2
({
req
(
design
())
req
(
physeq
())
data
<-
physeq
()
metaExpr
({
phyloseq_to_deseq2
(
data
,
design
=
..
(
design
()))})
})
dds
<-
metaReactive2
({
req
(
cds
())
metaExpr
({
DESeq2
::
DESeq
(
..
(
cds
()),
sfType
=
"poscounts"
)})
})
design
<-
metaExpr
({
as.formula
(
..
(
paste
(
"~"
,
input
$
deseqContrastVar
)))})
cds
<-
metaExpr
({
phyloseq_to_deseq2
(
data
,
design
=
design
)})
dds
<-
metaExpr
({
DESeq2
::
DESeq
(
cds
,
sfType
=
"poscounts"
)})
results
<-
metaReactive2
({
req
(
input
$
deseqContrastVar
)
req
(
dds
())
req
(
physeq
())
req
({
class
(
get_variable
(
physeq
(),
input
$
deseqContrastVar
))
==
"numeric"
||
length
(
input
$
deseqContrastMod
)
==
2
})
results
<-
if
(
class
(
get_variable
(
data
,
input
$
deseqContrastVar
))
==
"numeric"
)
{
data
<-
physeq
()
if
(
class
(
get_variable
(
data
,
input
$
deseqContrastVar
))
==
"numeric"
)
{
# First case: regression against a continuous variable
metaExpr
({
DESeq2
::
results
(
object
=
dds
,
DESeq2
::
results
(
object
=
..
(
dds
())
,
name
=
..
(
input
$
deseqContrastVar
),
tidy
=
TRUE
)
%>%
as_tibble
()
%>%
...
...
@@ -84,28 +89,34 @@ output$deseq <- metaRender2(renderPlot, {
inner_join
(
tax_table
(
data
)
%>%
as
(
"matrix"
)
%>%
as_tibble
(
rownames
=
"OTU"
),
by
=
"OTU"
)
})
}
else
{
validate
(
need
(
length
(
input
$
deseqContrastMod
)
==
2
,
"Invalid input."
))
if
(
length
(
levels
(
get_variable
(
data
,
input
$
deseqContrastVar
)))
==
2
)
{
# Second case: regression against a binary variable
metaExpr
({
DESeq2
::
results
(
object
=
dds
,
name
=
..
(
DESeq2
::
resultsNames
(
dds
)[
-1
]),
DESeq2
::
results
(
object
=
..
(
dds
())
,
name
=
..
(
DESeq2
::
resultsNames
(
..
(
dds
())
)[
-1
]),
tidy
=
TRUE
)
%>%
as_tibble
()
%>%
rename
(
OTU
=
row
)
%>%
inner_join
(
tax_table
(
data
)
%>%
as
(
"matrix"
)
%>%
as_tibble
(
rownames
=
"OTU"
),
by
=
"OTU"
)
})
}
else
{
# Third case: regression against a qualiative variable with three or more levels
metaExpr
({
DESeq2
::
results
(
object
=
dds
,
contrast
=
..
(
c
(
input
$
deseqContrastVar
,
input
$
deseqContrastMod
[
1
],
input
$
deseqContrastMod
[
2
])),
tidy
=
TRUE
)
%>%
as_tibble
()
%>%
rename
(
OTU
=
row
)
%>%
inner_join
(
tax_table
(
data
)
%>%
as
(
"matrix"
)
%>%
as_tibble
(
rownames
=
"OTU"
),
by
=
"OTU"
)
})
}
}
else
{
# Third case: regression against a qualiative variable with three or more levels
metaExpr
({
DESeq2
::
results
(
object
=
..
(
dds
())
,
contrast
=
..
(
c
(
input
$
deseqContrastVar
,
input
$
deseqContrastMod
[
1
],
input
$
deseqContrastMod
[
2
])),
tidy
=
TRUE
)
%>%
as_tibble
()
%>%
rename
(
OTU
=
row
)
%>%
inner_join
(
tax_table
(
data
)
%>%
as
(
"matrix"
)
%>%
as_tibble
(
rownames
=
"OTU"
),
by
=
"OTU"
)
})
}
}
})
detail
<-
metaReactive2
({
data
<-
physeq
()
detail
<-
if
(
class
(
get_variable
(
data
,
input
$
deseqContrastVar
))
==
"numeric"
)
{
if
(
class
(
get_variable
(
data
,
input
$
deseqContrastVar
))
==
"numeric"
)
{
# First case
metaExpr
({
..
(
paste0
(
"You compare low and high values of the continuous variable "
,
input
$
deseqContrastVar
,
".\nA positive log2FoldChange means more abundant for high values of "
,
input
$
deseqContrastVar
,
"."
))
...
...
@@ -123,16 +134,22 @@ output$deseq <- metaRender2(renderPlot, {
})
}
}
deseqTable
<-
metaExpr
({
})
})
output
$
deseq
<-
metaRender2
(
renderPlot
,
{
validate
(
need
(
physeq
(),
"Requires an abundance dataset"
),
need
(
class
(
get_variable
(
physeq
(),
input
$
deseqContrastVar
))
==
"numeric"
||
length
(
input
$
deseqContrastMod
)
==
2
,
"Requires a continuous design or a selection of two modalities for a discrete design."
)
#,
#need(class(results()) == "DESeqResults", "Invalid input.")
)
data
<-
physeq
()
deseqPlot
<-
metaExpr
({
ggplot
(
results
%>%
mutate
(
evidence
=
-
log10
(
padj
),
ggplot
(
..
(
results
())
%>%
mutate
(
evidence
=
-
log10
(
padj
),
evolution
=
case_when
(
padj
<=
..
(
input
$
deseqPadj
)
&
log2FoldChange
<
0
~
"Down"
,
padj
<=
..
(
input
$
deseqPadj
)
&
log2FoldChange
>
0
~
"Up"
,
padj
<=
0.05
&
log2FoldChange
<
0
~
"Down"
,
padj
<=
0.05
&
log2FoldChange
>
0
~
"Up"
,
TRUE
~
"Not DA"
)),
aes
(
x
=
log2FoldChange
,
y
=
evidence
))
+
...
...
@@ -140,20 +157,15 @@ output$deseq <- metaRender2(renderPlot, {
theme_bw
(
base_size
=
16
)
+
# clean up theme
theme
(
legend.position
=
"none"
,
# remove legend
plot.subtitle
=
element_text
(
size
=
12
))
+
# add subtitle
ggtitle
(
label
=
..
(
input
$
deseqTitle
),
subtitle
=
detail
)
+
# add informative title
ggtitle
(
label
=
..
(
input
$
deseqTitle
),
subtitle
=
..
(
detail
())
)
+
# add informative title
xlab
(
expression
(
log
[
2
](
"FoldChange"
)))
+
# x-axis label
ylab
(
expression
(
-
log
[
10
](
"adjusted p-value"
)))
+
# y-axis label
geom_vline
(
xintercept
=
0
,
colour
=
"grey80"
,
linetype
=
2
)
+
# add line at 0
geom_hline
(
yintercept
=
-
log10
(
..
(
input
$
deseqPadj
)
),
colour
=
"grey80"
,
linetype
=
2
)
+
geom_hline
(
yintercept
=
-
log10
(
0.05
),
colour
=
"grey80"
,
linetype
=
2
)
+
scale_color_manual
(
values
=
c
(
"Down"
=
"red"
,
"Not DA"
=
"grey20"
,
"Up"
=
"green"
))
# change colors
})
metaExpr
({
design
<-
..
(
design
)
cds
<-
..
(
cds
)
dds
<-
..
(
dds
)
results
<-
..
(
results
)
detail
<-
..
(
detail
)
p
<-
..
(
deseqPlot
)
p
})
...
...
@@ -176,3 +188,7 @@ observeEvent(input$deseq_output_code,
)
}
)
# output$deseqTable <- metaRender2(renderTable, {
# }
# )
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