library(shiny)

library(shinyjs)

library(plotly)

library(colourpicker)

library(shinythemes)

library(V8)

shinyUI(

fluidPage(theme = shinytheme('lumen'),

useShinyjs(),

img(src='Vasco_2.png', align = "left", height=100),

hr(),

tags$head(

tags$style(HTML("

"))

),

extendShinyjs(text = "shinyjs.refresh = function() { redir_Str = window.location.href.split('?')[0] + '?compare'; window.location.href = redir_Str ; }"),

# Application title

titlePanel('VASCO'),

#titlePanel(h1("VASCO", id="title")),

p("Visualization App for Single Cells explOration", id="titledescript"),

tabsetPanel( id = "main_panel",

# main panel for tSNE plot and group selection

tabPanel('Summary',

id = "tSNE",

# selected button!!

fluidRow(

br(),

# welcome text

column(8, offset = 1,

tags$div(

tags$p("This application facilitates real-time data visualization and exploration of single cell RNA-seq data.

It takes the gene-barcode matrix and the clustering result as input."),

tags$p("Users can:")

),

tags$ul(

tags$li("visualize the cells using t-distributed stochastic neighbour embedding (t-SNE) plots"),

tags$li("explore the expression pattern of specific genes"),

tags$li("investigate the identity of cell clusters by examining genes that are specific to a cluster")

)),

# main window plots

column(8,

plotlyOutput('tSNEPlot',height = '600px'),

# we may not want the barchart displayed; see issue#30

# plotlyOutput('countPerCluster'),

br(),

offset=2)

)),

# panel for displaying individual gene expression data

tabPanel('Visualize genes',

id = "geneEpxr",

column(4, wellPanel(selectizeInput('input_genes', h1('Select genes'),

choices = list_of_genesymbols,

options = list(maxItems = geneExpr_maxItems),

selected = c('LGALS1_ENSG00000100097'),

multiple = TRUE),

actionButton("exprGeneButton", "Visualize"),

div(id = 'tsneHeatmapOptions',

sliderInput("MinMax", label= h5("Adjust heatmap color scale:"), min = 0, max = 1, value = c(0,0.4), step= 0.02),

sliderInput("Midpoint", label= h5("Adjust midpoint of color scale:"), min = 0, max = 1, value = 0.1, step= 0.02),

colourInput("colmax", "Select color of scale maximum", value = geneExpr_colorMax),

colourInput("colmid", "Select color of scale midpoint", value = geneExpr_colorMid),

colourInput("colmin", "Select color of scale minimum", value = geneExpr_colorMin)

)

)

),

column(8,

tabsetPanel(id ='exprVis',

tabPanel('tSNE heatmap', value = 'tSNE',

uiOutput("geneExprPlot")),

tabPanel('Box plots', value = 'box',

plotlyOutput("geneExprGeneCluster"))))

),

# exploration of selection

tabPanel( 'Explore clusters',

id= 'Compare',

tabsetPanel(tabPanel('Compare',

column(3,wellPanel(

h4(id = "select_text", "Please select first group"),

actionButton(inputId = "pop_one_selected", label = "Save group 1"),

actionButton(inputId = "pop_two_selected", label = "Save group 2"),

br(),

div( id = 'definedInputSelection',

checkboxInput(inputId = 'selectDefinedGroup',

value = F,

label = 'Select predefined cluster(s) for group 1'),

checkboxGroupInput(inputId = 'whichGroups',

label = 'Predefined clusters:',

choices = unique(tsne$id) %>% sort)

),

downloadButton(outputId = 'downloadDifGenes', label = 'Download'),

br(),

br(),

actionButton(inputId = "reload", label = "Select new groups"))),

column(9,

div(id= "div_select_one", plotlyOutput('tSNE_select_one',height = '600px')),

div(id = "div_select_two", plotlyOutput('tSNE_select_two',height = '600px')),

dataTableOutput('difGeneTable'),

div(id= 'comparisonOutput',

tabsetPanel(tabPanel('Visualize genes',

id = "histPlot",

plotlyOutput('histPlot', height = '500px')),

tabPanel('Visualize selected groups',

id = 'tSNE plot',

plotlyOutput('tSNE_summary'),

plotlyOutput('cell_type_summary')

)

)

)

)),

tabPanel('Create',

column(3,

textInput(inputId = 'newClusterName',label ='New name'),

h4(id = 'selectTextForRename', 'Please select group to rename'),

actionButton(inputId = 'renamePoulationButton',label = 'Rename Selection'),

checkboxInput(inputId = 'selectDefinedGroupForRename',

value = F,

label = 'Select predefined cluster(s)'),

checkboxGroupInput(inputId = 'whichGroupsForRename',

label = 'Predefined clusters:',

choices = unique(tsne$id) %>% sort)),

column(9,

plotlyOutput('tSNE_selectForRename',height = '600px')))

)

),

tabPanel( 'Upload data',

id= 'upload',

sidebarPanel(fileInput('barcodes_file', 'Barcodes .tsv File',

accept=c('text/tsv',

'text/comma-separated-values,text/plain',

'.tsv')),

fileInput('genes_file', 'Genes .tsv File',

accept=c('text/tsv',

'text/comma-separated-values,text/plain',

'.tsv')),

fileInput('tsne_file', 'tsne tdf File',

accept = NULL),

fileInput('mtx_file', 'Expression matrix .mtx File',

accept=c(

'.mtx')),

actionButton(inputId = "upload_button", label = "Submit Data")

)

)

)

)

)