Skip to content

Commit

Permalink
documentation added
Browse files Browse the repository at this point in the history
  • Loading branch information
SoniaRuiz committed Feb 15, 2023
1 parent 128505c commit 7629597
Show file tree
Hide file tree
Showing 2 changed files with 183 additions and 442 deletions.
98 changes: 13 additions & 85 deletions introverse/app.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -45,18 +45,16 @@ ui <- navbarPage(
useShinyjs(),
tags$head(includeHTML(path = "www/html/google-analytics.html")),

#tags$head(tags$link(rel="shortcut icon", href = "introverse-icon.png")),

header = list(shiny::includeCSS(path = "www/css/style.css"),
shiny::includeScript(path = "www/js/api.js")
),
#shinyFeedback::useShinyFeedback(),

title = "IntroVerse",
id = "introverse",
selected = "landing",



theme = bslib::bs_theme(bootswatch = "cosmo",
version = 4),

Expand Down Expand Up @@ -104,21 +102,6 @@ ui <- navbarPage(
div(
id = "geneInputPanel_tab1",

# ## Option 1
# hr(),
# span(strong("Search:")),
# shiny::radioButtons(inputId = "radiobutton_introntype_tab1",
# label = "",
# choiceNames = c("Introns",
# "Novel Junctions"),
# choiceValues = c("introns",
# "novel"),
# selected = "introns"),

#strong(span("Using Ensembl Release 105 (Dec 2021)")),

#hr(),

## Option 1
span(strong("Search by:"),
a(`data-toggle`="collapse",
Expand Down Expand Up @@ -189,8 +172,6 @@ ui <- navbarPage(

hr(),



## Option 4

p(strong("Sample selection"),
Expand Down Expand Up @@ -232,8 +213,7 @@ ui <- navbarPage(

hr(),


## Option 6
## Option 5
p(strong("Support for novel annotation"),
a(`data-toggle`="collapse",
href="#collapseNovelAnnotation",
Expand All @@ -258,10 +238,7 @@ ui <- navbarPage(
),
hr(),




## Option 5
## Option 6

span(strong("Additional filters"),
a(`data-toggle`="collapse",
Expand All @@ -280,9 +257,6 @@ ui <- navbarPage(
value = F)
),




## BUTTON
hr(),
actionButton(inputId = "geneButton_tab1", label = "Accept"),
Expand Down Expand Up @@ -408,7 +382,6 @@ ui <- navbarPage(




br(),

uiOutput("use_case3"),
Expand Down Expand Up @@ -541,15 +514,16 @@ ui <- navbarPage(

h3("introverse.sqlite"),
p("To download this resource, please click the button below:"),
downloadButton(outputId = 'downloadSQLite', label = 'Download', class = 'disabled' ),br(),
downloadButton(outputId = 'downloadSQLite', label = 'Download' ),br(),
p(tags$small("The download may take a few seconds to start.", style="font-size: smaller")),

p("This resource contains:"),
tags$ul(
tags$li("The full IntroVerse database in SQLite format ", em("('introverse.sqlite')"), "."),
tags$li("The SQLite schema, to provide information of how the different child and master tables are related between them ", em("('introverse_schema_complete.html')"), "."),
tags$li("Two .csv files containing the column description of the intron and novel junction tables ", em("('intron_columns.csv' and 'novel_columns.csv')"), "."),
tags$li("A .txt file with some useful SQL queries ", em("('sql_queries.txt')"), ".")
tags$li("A .txt file with some useful SQL queries ", em("('sql_queries.txt')"), "."),
tags$li("A .txt file containing the complete SQL schema ", em("('introverse_sql_schema.txt')"), ".")
)))),
tabPanel(
title = "SQLite Schema",
Expand Down Expand Up @@ -657,14 +631,8 @@ server <- function(input, output, session) {
shinyjs::hideElement(id = "chr_strand_tab1")
shinyjs::hideElement(id = "start_end_tab1")
shinyjs::hideElement(id = "div_gene_file")
#shinyjs::hideElement(id = "gene_tab1")
# shinyjs::disable(id = "geneButton")


#shinyjs::hideElement(id = "geneInputPanel_tab1")
#shinyjs::hideElement(id = "genePanel_tab1")

shinyjs::disable(id = "threshold_tab1")
#shinyjs::disable(id = "radiobutton_searchtype_tab1")


##############################################################################
Expand Down Expand Up @@ -694,7 +662,6 @@ server <- function(input, output, session) {
shinyjs::hideElement(id = "start_end_tab1")


# shiny::updateSliderInput(session = session, inputId = "threshold_tab1", value = 1)
if (!input$all_tissues_tab1) {
shinyjs::enable(id = "data_bases_tab1")
}
Expand All @@ -709,7 +676,6 @@ server <- function(input, output, session) {
shinyjs::showElement(id = "start_end_tab1")


#shiny::updateSliderInput(session = session, inputId = "threshold_tab1", value = 1)
if (!input$all_tissues_tab1) {
shinyjs::enable(id = "data_bases_tab1")
}
Expand Down Expand Up @@ -907,8 +873,9 @@ server <- function(input, output, session) {
#print(URLdecode(URL = input$cluster_tab1))

novel_junctions_from_intron <- get_novel_data_from_intron(intron_id = URLdecode(URL =input$intronID_tab1),
db = URLdecode(URL =input$db_tab1),
sample_group = URLdecode(URL =input$cluster_tab1)) %>% dplyr::mutate(More = "")
clust = URLdecode(URL =input$cluster_tab1),
db = URLdecode(URL =input$db_tab1)) %>%
dplyr::mutate(More = "")
novel_tooltips <- read.delim(file = "./dependencies/novel_tooltips.csv", header = T, sep = ",") %>%
as_tibble()

Expand Down Expand Up @@ -978,15 +945,6 @@ server <- function(input, output, session) {
## MODAL POP-UPS
##############################################################################

# output$modalVisualiseTranscript_tab1 <- renderPlot({
#
# visualise_transcript(intron_id = str_replace_all(string = input$intronID_tab1, pattern = "%20", replacement = " "),
# db = str_replace_all(string = input$db_tab1, pattern = "%20", replacement = " "),
# clust = str_replace_all(string = input$cluster_tab1, pattern = "%20", replacement = " ") )
#
#
# }, width = "auto", height = "auto")

visualiseTranscriptPlot <- function() {
visualise_transcript(novel_id = str_replace_all(string = input$novelID_tab1, pattern = "%20", replacement = " "),
db = str_replace_all(string = input$db_tab1, pattern = "%20", replacement = " "),
Expand Down Expand Up @@ -1261,7 +1219,7 @@ server <- function(input, output, session) {

tagList(
h1(em(input$gene_tab1)),
h2("Mis-splicing activity in the MANE transcript"),
h2("Mis-splicing activity in the MANE transcript of ", em(input$gene_tab1)),
br(),
p("The Mis-Splicing Ratio (MSR) measure represents the frequency whereby any annotated intron within the Matched Annotation from NCBI and EMBL-EBI (MANE) transcript of a gene of interest is mis-spliced at its donor (in blue - MSR_Donor) and acceptor (in red - MSR_Acceptor) splice sites across all samples of a given human tissue."),
p("Since the MSR formula produces a normalised figure ranging between 0 and 1, the higher the vertical bar shown, the higher the proportion of novel junction reads paired to the annotated intron displayed.",
Expand Down Expand Up @@ -1293,20 +1251,7 @@ server <- function(input, output, session) {
}, width = "auto", height = "auto")

}





# downloadHandler(
# filename = paste0("missplicing_",i,".png"),
# content = function(file) {
# ggsave(file, plot = plot_graph, device = "png")
# }, contentType = 'image/png')



#outputtt$`25`

}),
shinyjs::enable(id = "geneButton_tab1"),
shinyjs::removeClass(class = "disabled-tab",
Expand Down Expand Up @@ -1348,24 +1293,7 @@ server <- function(input, output, session) {
rownames = F)
)
)
# i <- metadata$SRA_project_tidy %>% unique() %>% length()
#
# #metadata <- plot_metadata()
# tagList(
#
# lapply(1:i, function(n) {
#
# metadata <- plot_metadata()
# total <- metadata$SRA_project_tidy %>% unique()
# df <- metadata %>%
# dplyr::filter(SRA_project_tidy == total[n])
# #print(total[n])
# #outputtt[[paste(n)]]
# shiny::tags$h3(total[n]) %>% print
# DT::renderDT(server = F, DT::datatable(df))
# #outputtt$`25`
# })
# )

})

output$intron_table <- DT::renderDataTable({
Expand Down
Loading

0 comments on commit 7629597

Please sign in to comment.