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ui.R
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ui.R
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library(shiny)
library(shinyjs)
library(data.table)
library(rjson)
library(htmlwidgets)
library(chromatography)
library(stringr)
library(stringi)
library(DT)
library(shinyBS)
#source("JS.R")
shinyUI(
fluidPage(
useShinyjs(),
theme = "simplex3.3.6.css", # http://bootswatch.com/ | sandstone/simplex/flatly/darkly
tags$head(
includeCSS("www/samples.css"),
includeHTML("www/google-analytics.html"),
tags$head(HTML("<link href='https://fonts.googleapis.com/css?family=Inconsolata' rel='stylesheet' type='text/css'>")),
tags$title("GLASS"),
tags$meta(name="description", content="web-based Sanger sequence trace viewer, editor, aligner and variant caller"),
tags$meta(name="keywords", content="Sanger,sequence,TP53,D3.js,Shiny,trace,chromatogram"),
tags$script('window.onbeforeunload = function() {
return "You will need to start over if you navigate away!";
};'),
tags$script('Shiny.addCustomMessageHandler("resetFileInputHandler", function(x) {
var el = $("#" + x);
el.replaceWith(el = el.clone(true));
var id = "#" + x + "_progress";
$(id).css("visibility", "hidden");
});'),
tags$style(HTML(".DTFC_LeftBodyLiner { width: 100% !important; }"))
),
fluidRow(
#HTML("<div style=\"background-color:#fee0d2\" class=\"alert alert-dismissible alert-primary\">
# <button type=\"button\" class=\"close\" data-dismiss=\"alert\">×</button>
# <strong>Important update released on 2018-November-2</strong>, see changelog for details, contact us directly via <a href=mailto:[email protected] target='_blank'>email</a> if needed.
# </div>"),
column(1, HTML("  <b><font size=6em>GLASS</font></b>")),
column(1,HTML('<div style="padding:.3em .5em"><a href="javascript:void(0)" id="app-disclaimer-link" onclick="$(\'#disclaimer-modal\').modal(\'show\')" >
ver 0.4.8 <br> (2023-Mar-24)
</a></div>'),
includeHTML("www/log.html")
),
column(10, HTML("<br><font size=2em>   | R&D by <a href=http://bat.infspire.org target=_blank>bat.infspire.org</a>  <font size=0.9em>&</font>  <a href=https://www.ceitec.eu/medical-genomics-sarka-pospisilova/rg34 target=_blank>Medical Genomics @ CEITEC MU</a>  <font size=0.9em>&</font>  <a href=http://www.ericll.org target=_blank>ERIC</a>  <font size=0.9em>&</font>  <a href=http://www.igcll.org target=_blank>IgCLL group</a></font>   | IT by <a href=https://metavo.metacentrum.cz/en/ target='_blank'>CESNET/MetaCentrum</a>   | <a href=mailto:[email protected] target='_blank'>email us</a> | <a href=https://www.ncbi.nlm.nih.gov/pubmed/29036643 target='_blank'>cite us</a>"))
),
fluidRow(
column(2, HTML(paste(" <i>assisted & standardised assessment</br>  of gene variations from Sanger data</i></br></br>"))),
column(9, htmlOutput("files"))
),
tabsetPanel(id = 'tabs',
tabPanel('files',value = 'smpl_brws',icon = icon("archive"),
fluidRow(
column(1,
HTML("<div style='display:inline;'><h5 style='display:inline;float:right;'>quick guide</h5></div>")
),
column(11,wellPanel(tags$div(HTML(paste("<div style=\"font-family:'Inconsolata';font-size:1.1em;\">
 (0) hovering over '[?]'s will provide quick help tips </br>
 (1) select / upload relevant references beforehand, GLASS will align and auto-orientate against them </br>
 (2) upload ABI files from supported references, forward and/or reverse, and with unique names </br>
 (3) after processing and auto-detection of most file properties, pair / unpair / swap / delete / change reference as necessary </br>
 (4) click the blue 'play' button to load the file(s) </br>
 (5) when done in 'variants' panel (find separate instructions there), confirmed variants will appear under 'status' and are exportable with the green 'export variants' button
</div>"), sep = ""))))
)
,br()
,fluidRow(
column(1,
HTML(paste("<hr><div style='display:inline;'><h4 style='display:inline;'>references</h4>   <b style='display:inline;' id ='ref_help'> [?]</b></div>"))
),
column(11,
# tags$div(title="",HTML(paste("<hr><div style='display:inline;'><h4 style='display:inline;'>references</h4>   <b style='display:inline;' id ='ref_help'> [?]</b></div>")))
# checkboxInput("showWP3", HTML("Manage References <i class='fa fa-wrench' aria-hidden='true'></i>")),
# conditionalPanel(condition="input.showWP3",
fluidRow(
column(3,
selectizeInput("additionalRefs", "select from our list of curated references",c("TP53","ATM","NOTCH1","CALR"), selected = c("TP53"), multiple = TRUE,
options = list(maxItems = 4))
),
column(3, fileInput("custom_gb",label = HTML("OR upload your own GenBank file<b style='display:inline; color:red;' id ='q1'> [?!]</b>"),
multiple=F,accept=c('.gb','.gbk'),width = '100%')
)
),
# )
HTML("currently selected references"),
uiOutput("alignTo_new")
)
)
,br()
,fluidRow(
column(1,tags$div(title="",HTML(paste("<hr><div style='display:inline;'><h4 style='display:inline;'>samples</h4>   <b style='display:inline;' id ='samples_ui'> [?]</b></div>"))))
,column(6,
fileInput("browser_files","upload .abi or .ab1 files with unique names",multiple=T,accept=c('.abi','.ab1'),width = '100%'))
,column(2,
tags$div(title="The list of confirmed variants can be exported and saved in the form of an Excel table."
,downloadButton('export_btn','export variants [?]',class = "exp_btn")))
,DT::dataTableOutput('samples_table')
)
),
tabPanel('variants', value = 'main', icon = icon("search"), # http://fontawesome.io/icons/
fluidRow(
column(4,
column(3,
# this should be replaced by direct interaction with graph or data table
tags$div(title="",
textInput("choose_call_pos",HTML("<div>call position <b id = 'call_pos_help'>[?]</b></div>"))),
tags$div(title="",
selectInput("change_user_sample",HTML("<div>change variants <b id = 'change_user_help'>[?]</b></div>"),choices=list("",deletion="-","A","T","G","C","S (G or C)"="S","W (A or T)"="W","R (A or G)"="R","Y (C or T)"="Y","K (G or T)"="K","M (A or C)"="M","B (C or G or T)"="B","V (A or C or G)"="V","H (A or C or T)"="H","D (A or G or T)"="D","N"),selected="",selectize=F,size=1),
selectInput("change_user_mut",NULL,choices=list("",deletion="-","A","T","G","C","S (G or C)"="S","W (A or T)"="W","R (A or G)"="R","Y (C or T)"="Y","K (G or T)"="K","M (A or C)"="M","B (C or G or T)"="B","V (A or C or G)"="V","H (A or C or T)"="H","D (A or G or T)"="D","N"),selected="",selectize=F,size=1),
# textInput("change_variant","change variant to"),
actionButton("change_btn","change", icon = icon("exchange"), width='100%'))
),
column(9,
tags$div(title="",
HTML("<div>general infobox <b id = 'general_infobox_help'>[?]</b></div>")),
verbatimTextOutput("infobox")
)
),
column(8,
column(2,
tags$div(title=""
,HTML(paste("<div>heterozygous</br>insertion(s)/deletion(s) <b id = 'hetero_indel_help'>[?]</b></div>"))
,verbatimTextOutput("hetero_indel_pid")
# ,conditionalPanel(condition = "!output.indels_present",
# HTML("<font color=lightgrey><i>if indels detected, checkbox will appear</i></font>")
# )
,conditionalPanel(condition = "output.hetero_indel_pid == 'detected'",
div(style="display: inline-block;vertical-align:top;" ,actionButton("hetero_use_lnk", "pinpoint indel(s)"))
, div(style="display: inline-block;vertical-align:top;" ,HTML(paste("<div><b id = 'hetero_use_lnk_help'>[?]</b></div>"))
)
)
)
),
column(2,
tags$div(title="",
sliderInput("mut_min",HTML("<font style='font-size:16px;'>detection limit</font>   <b id= mut_min_help> [?]</b><br><br>"), ticks=FALSE, min = 0, max = 50, value = 10, step = 0.5, round = 1, post='%', width="90%")
,conditionalPanel(condition = "output.indels_present"
,tags$div(title="",
checkboxInput("incorporate_checkbox",HTML("align secondary peaks <b id = use_indels_help >[?]</b>"), value = F)
)
)
)
),
column(5,
column(1),
column(6
,column(12,
tags$div(title="",HTML("trimming: ignore sequence positions ... <b id = trim_help >[?]</b>")))
,column(6
,numericInput("trim_fwd_start","fwd, up to",value = 0,min = 0,max=1000)
,numericInput("trim_rev_start","rev, up to",value = 0,min = 0,max=1000)
)
,column(6
,numericInput("trim_fwd_end", "fwd, after",value = 1000,min = 1,max=1000)
,numericInput("trim_rev_end", "rev, after",value = 1000,min = 1,max=1000)
)
),
column(1),
column(4,
sliderInput("qual_thres_to_call","min base quality", ticks=FALSE, min = 0, max = 50, value = 0)
,tags$div(title="",
sliderInput("s2n_min",HTML("min signal/noise <b id = min_sn_help>[?]</b>"), ticks=FALSE, min = 0, max = 10, value = 2, step = 0.1, round = 1)
)
#sliderInput("qual_thres_to_trim","[qual thres to trim]", ticks=FALSE, min = 0, max = 60, value = 0)
)
),
column(3,
column(1),
column(6
,checkboxInput("show_qual_checkbox","show quality", value = F)
,checkboxInput("show_calls_checkbox","show calls", value = F)
,conditionalPanel(condition = "output.reverse",
checkboxInput("join_traces_checkbox","join traces", value = F))
#sliderInput("opacity_fwd","fwd trace opacity", ticks=FALSE, min = 0, max = 100, value = 100, step = 5),
),
column(1),
column(4
,sliderInput("max_y_p","peak height", ticks=FALSE, min = 1, max = 400, value = 100, step = 10)
,conditionalPanel(condition = "output.reverse && input.join_traces_checkbox" ,
sliderInput("opacity","R <trace opacity> F", ticks=FALSE, min = -100, max = 100, value = 0, step = 10))
,conditionalPanel(condition = "!input.join_traces_checkbox", HTML("<div id='spacer'> </div>"))
#,uiOutput('helpButton')
#,actionButton("toggle_help",icon = icon("question"), "hide help",class = "show_hide_help")
,tags$style(HTML("#spacer{margin-top:43px;}"))
)
)
)
),
fluidRow(
# === following lines left out of text bc of space ===
# "| horizontal grey line = full sequence |"
# | <font color=brown>brown dots</font> = intensity anomalies (indels?)
#input.toggle_help % 2 == 0
conditionalPanel("input.toggle_help % 2 == 0",column(12,wellPanel(tags$div(HTML(paste("<div style=\"font-family:'Inconsolata';font-size:1.1em;\">
<b>minimap     </b>: <font color=#4682B4>blue box = resize/move for navigation</font> | boxes = exons/introns | horizontal grey line = full sequence | verticals = variants, ref>pri>sec | <font color=red>red dotted lines</font> = filtered noisy beginnings</br>
<b>chromatogram</b>: click text to print info^ | crosshair + click = drag | zoom-in for extra info (coords..) | sequences, from top = ref, call/pri, mut/sec | pink verticals = variants | grey bars = codons</br>
<b>variants    </b>: 'goto' = go to variant on chromatogram | 'x' = ignore for the session | 'confirm' = keep for the session (even if you change parameters) and make them exportable from 'samples' panel
</div>
"), sep = "")))))
),
chromatographyOutput("plot"),
DT::dataTableOutput("chosen_variants_table"),
#conditionalPanel(condition=" output.chosen_variants_table ",downloadButton("export_btn","export")),
br()
)
,tabPanel('heterozygous alignment', value = 'aln', icon = icon("sliders"),
verbatimTextOutput("aln"),
plotOutput('het_histogram',height = 600)
)
,tabPanel('help', value = 'help', icon = icon("question"),
# selectInput("img_help","choose a topic:",choices=c("File Upload","Select ref from list","Load custom GenBank ref.","Scroll","Zoom","Export detected variant"))
selectInput("img_help","choose a topic:",choices=c("select ref from list","load custom GenBank ref","file upload","scroll","zoom","export detected variants"))
,uiOutput("upload_file")
)
# tabPanel('variant annotation', value = 'annotation', icon = icon("user-md")
# ),
# ,
# tabPanel('calls', value = 'call_table', icon = icon("table"),
# shiny::dataTableOutput("call_table")
# )
# ,tabPanel('intensities fwd', value = 'intens_table', icon = icon("table"),
# shiny::dataTableOutput("intens_table")
# )
# ,tabPanel('intensities rev', value = 'intens_table_rev', icon = icon("table"),
# shiny::dataTableOutput("intens_table_rev")
# )
),
bsModal("modalnew", "Change name", "BUTnew", size = "small",
HTML("Do you want to change the name?"),
actionButton("BUTyes", "Yes"),
actionButton("BUTno", "No")
)
)
)