Skip to content
GitLab
Menu
Projects
Groups
Snippets
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
umrf
ranomaly
Commits
83d2e38e
Commit
83d2e38e
authored
Nov 09, 2021
by
Sebastien Theil
Browse files
add plotly libraries.
parent
9d041991
Changes
2
Hide whitespace changes
Inline
Side-by-side
NAMESPACE
View file @
83d2e38e
...
...
@@ -49,7 +49,6 @@ import(metagenomeSeq)
import(mixOmics)
import(pairwiseAdonis)
import(phyloseq)
import(plotly)
import(psadd)
import(reshape2)
import(scales)
...
...
@@ -93,6 +92,7 @@ importFrom(phangorn,dist.ml)
importFrom(phangorn,phyDat)
importFrom(phangorn,pml)
importFrom(plotly,ggplotly)
importFrom(plotly,plot_ly)
importFrom(ranacapa,ggrare)
importFrom(reshape2,melt)
importFrom(venn,venn)
R/bars_fun.R
View file @
83d2e38e
...
...
@@ -7,7 +7,7 @@
#'
#' @return A plotly graph.
#'
#' @import plotly
#' @import
From
plotly
ggplotly
#' @importFrom ranacapa ggrare
#'
#' @export
...
...
@@ -45,7 +45,7 @@ rarefaction <- function(data = data, col = NULL, step = 100, ggplotly = TRUE){
#'
#' @return Returns barplots in an interactive plotly community plot
#'
#' @import plotly
#' @import
From
plotly
plot_ly subplot layout
#' @importFrom microbiome aggregate_top_taxa
#' @importFrom reshape2 melt
#' @importFrom gtools mixedsort
...
...
@@ -111,7 +111,7 @@ bars_fun <- function(data = data, rank = "Genus", top = 10, Ord1 = NULL, Fact1 =
color
=
~
g
,
legendgroup
=
~
g
,
showlegend
=
FALSE
)
%>%
layout
(
xaxis
=
list
(
zeroline
=
FALSE
,
showline
=
FALSE
,
showgrid
=
FALSE
),
)
%>%
plotly
::
layout
(
xaxis
=
list
(
zeroline
=
FALSE
,
showline
=
FALSE
,
showgrid
=
FALSE
),
yaxis
=
list
(
showticklabels
=
FALSE
,
title
=
""
,
showgrid
=
FALSE
))
...
...
@@ -126,21 +126,20 @@ bars_fun <- function(data = data, rank = "Genus", top = 10, Ord1 = NULL, Fact1 =
meltdat
$
variable
=
factor
(
meltdat
$
variable
,
levels
=
c
(
"Other"
,
tt
[
tt
!=
"Other"
]))
p1
=
plot_ly
(
meltdat
,
x
=
~
sample.id
,
y
=
~
value
,
type
=
'bar'
,
name
=
~
variable
,
color
=
~
variable
)
%>%
#, color = ~variable
layout
(
title
=
"Relative abundance"
,
yaxis
=
list
(
title
=
'Relative abundance'
),
xaxis
=
xform
,
barmode
=
'stack'
)
plotly
::
layout
(
title
=
"Relative abundance"
,
yaxis
=
list
(
title
=
'Relative abundance'
),
xaxis
=
xform
,
barmode
=
'stack'
)
if
(
length
(
df1
$
x
)
!=
length
(
unique
(
df1
$
g
))){
p1
<-
subplot
(
p1
,
subp1
,
nrows
=
2
,
shareX
=
T
,
heights
=
c
(
0.95
,
0.05
))
%>%
layout
(
xaxis
=
xform
)
p1
<-
plotly
::
subplot
(
p1
,
subp1
,
nrows
=
2
,
shareX
=
T
,
heights
=
c
(
0.95
,
0.05
))
%>%
plotly
::
layout
(
xaxis
=
xform
)
}
}
else
{
#raw abundance
plottitle
=
"Raw abundance"
p1
=
plot_ly
(
meltdat
,
x
=
~
sample.id
,
y
=
~
value
,
type
=
'bar'
,
name
=
~
variable
,
color
=
~
variable
)
%>%
#, color = ~variable
layout
(
title
=
"Raw abundance"
,
yaxis
=
list
(
title
=
'Raw abundance'
),
xaxis
=
xform
,
barmode
=
'stack'
)
plotly
::
layout
(
title
=
"Raw abundance"
,
yaxis
=
list
(
title
=
'Raw abundance'
),
xaxis
=
xform
,
barmode
=
'stack'
)
if
(
length
(
df1
$
x
)
!=
length
(
unique
(
df1
$
g
))){
p1
<-
subplot
(
p1
,
subp1
,
nrows
=
2
,
shareX
=
T
,
heights
=
c
(
0.95
,
0.05
))
%>%
layout
(
xaxis
=
xform
)
p1
<-
plotly
::
subplot
(
p1
,
subp1
,
nrows
=
2
,
shareX
=
T
,
heights
=
c
(
0.95
,
0.05
))
%>%
plotly
::
layout
(
xaxis
=
xform
)
}
}
...
...
@@ -160,8 +159,8 @@ bars_fun <- function(data = data, rank = "Genus", top = 10, Ord1 = NULL, Fact1 =
color
=
~
variable
,
legendgroup
=
~
variable
,
showlegend
=
(
.y
==
levels
(
meltdat
[,
Ord1
])[
1
])),
keep
=
TRUE
)
%>%
subplot
(
nrows
=
1
,
shareX
=
TRUE
,
shareY
=
TRUE
,
titleX
=
FALSE
)
%>%
layout
(
title
=
plottitle
,
plotly
::
subplot
(
nrows
=
1
,
shareX
=
TRUE
,
shareY
=
TRUE
,
titleX
=
FALSE
)
%>%
plotly
::
layout
(
title
=
plottitle
,
xaxis
=
list
(
title
=
glue
(
"{Ord1} = {unique(meltdat[, Ord1])[1]}"
)),
yaxis
=
list
(
title
=
'Relative abundance'
),
barmode
=
'stack'
)
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment