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migale
affiliationExplorer
Commits
885ff605
Commit
885ff605
authored
Jan 21, 2020
by
Sandra Derozier
Browse files
V1 - Upload Biom & TSV files / ASV selection
parent
93850786
Changes
4
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Inline
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R/app_server.R
View file @
885ff605
#' @import shiny
app_server
<-
function
(
input
,
output
,
session
)
{
app_server
<-
function
(
input
,
output
,
session
)
{
# Load package data in the session (for testing purpose)
# data("physeq", package = "affiliationExplorer")
# data("affi", package = "affiliationExplorer")
# data("otu_dictionary", package = "affiliationExplorer")
# List the first level callModules here
}
observeEvent
(
input
$
tsv
,
{
# Read the biom file --> phyloseq
biomfile
<-
read_frogs_biom
(
input
$
biom
$
datapath
)
# Read the tsv file --> readr
multihits
<-
read_multihits
(
input
$
tsv
$
datapath
)
#
all
<-
sanitize_physeq_and_affi
(
biomfile
,
multihits
)
# Add ASV Select Input
insertUI
(
selector
=
"#tmp"
,
where
=
"beforeEnd"
,
ui
=
selectInput
(
"asv"
,
label
=
"Select ASV"
,
choices
=
all
$
otu_dictionary
$
OTU
,
multiple
=
FALSE
)
)
observeEvent
(
input
$
asv
,
{
# Extract Affiliation for a given OTU
data
<-
extract_affiliation
(
all
$
affi
,
input
$
asv
)
amb
<-
find_level
(
data
)
output
$
txt
<-
renderUI
({
paste
(
input
$
asv
,
"- "
,
nrow
(
data
)
,
" affiliation, ambiguity at rank "
,
amb
)})
output
$
table
<-
renderTable
({
data
})
# output$table <- renderFlexTable({
# mymtcars$Name <- paste0('<label><input type="radio" id="name', seq_along(names(data)), '"> <span>', names(data), '</span></label>')
# })
})
})
}
\ No newline at end of file
R/app_ui.R
View file @
885ff605
#' @import shiny
#' @import shinycssloaders
#' @import shinydashboard
app_ui
<-
function
()
{
tagList
(
# Leave this function for adding external resources
golem_add_external_resources
(),
# List the first level UI elements here
fluidPage
(
h1
(
"affiliationExplorer"
)
dashboardPage
(
skin
=
"purple"
,
# DashBooard Header
dashboardHeader
(
title
=
"Affiliation explorer"
),
# DashBooard Sidebar
dashboardSidebar
(
fileInput
(
"biom"
,
"Upload Biom File"
,
accept
=
c
(
".biom"
)
),
fileInput
(
"tsv"
,
"Upload MultiHits TSV File"
,
accept
=
c
(
"text/csv"
,
".tsv"
)
),
textOutput
(
"tmp"
)
),
# DashBooard Body
dashboardBody
(
fluidPage
(
fluidRow
(
box
(
title
=
"Affiliation selection"
,
width
=
NULL
,
status
=
"primary"
,
solidHeader
=
T
,
htmlOutput
(
"txt"
),
HTML
(
"<br/>"
),
tableOutput
(
"table"
)
)
)
)
)
)
)
}
...
...
@@ -13,6 +45,8 @@ app_ui <- function() {
#' @import shiny
golem_add_external_resources
<-
function
(){
tags
$
link
(
rel
=
"stylesheet"
,
type
=
"text/css"
,
href
=
"www/custom.css"
)
addResourcePath
(
'www'
,
system.file
(
'app/www'
,
package
=
'affiliationExplorer'
)
)
...
...
dev/02_dev.R
View file @
885ff605
...
...
@@ -7,14 +7,16 @@
## 2.1 Add modules
##
golem
::
add_module
(
name
=
"my_first_module"
)
# Name of the module
golem
::
add_module
(
name
=
"my_other_module"
)
# Name of the module
golem
::
add_module
(
name
=
"Main"
)
# Name of the module
## 2.2 Add dependencies
## Allow pipe use
usethis
::
use_pipe
()
usethis
::
use_package
(
"shinydashboard"
)
#usethis::use_package("shinycssloaders")
#usethis::use_package("ReporteRs")
usethis
::
use_package
(
"phyloseq"
)
# To call each time you need a new package
usethis
::
use_package
(
"biomformat"
)
usethis
::
use_package
(
"dplyr"
)
...
...
dev/run_dev.R
View file @
885ff605
# Set options here
options
(
golem.app.prod
=
FALSE
)
# TRUE = production mode, FALSE = development mode
options
(
shiny.maxRequestSize
=
80
*
1024
^
2
)
options
(
spinner.color
=
"#0275D8"
,
spinner.color.background
=
"#ffffff"
,
spinner.size
=
2
)
# Detach all loaded packages and clean your environment
golem
::
detach_all_attached
()
...
...
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