tabItem(tabName = "qcFilterTab",
fluidRow(
column(12,
h3(strong("QC & Filter (Preprocessing)")),
hr(),
wellPanel(
column(12,
tags$div(class = "",
h4(strong("Filter Cells")),
p("Seurat allows you to easily explore QC metrics and filter cells based on any user-defined criteria.
You can visualize gene and molecule counts, plot their relationship, and exclude cells with a clear outlier number of genes detected as potential multiplets.
This is not a guaranteed method to exclude cell doublets, see tutorial for more information.
As an example in the tutorial, you can filter cells based on the percentage of mitochondrial genes present."),
hr(),
h4("Filter Options:"),
tags$div(class = "BoxArea2",
h4(strong("1) By Regular Expression:")),
column(7,
wellPanel(
column(12,
column(6,
textInput("regexFilter", "By Regex Expression",
placeholder = "Eg. ^MT- for genes that start with 'MT-'")
),
column(6,
textInput("regexFilterLabel", "Label (no spaces)",
placeholder = "Eg. mito")
)
)
,
column(12,
column(6,
actionButton("testExpr","Test Regex", class = "button-primary button-pill",style = "width: 100%;")
),
column(6,
conditionalPanel("input.regexFilter.length > 0 && input.regexFilterLabel.length > 0",
actionButton("addExpr","Add Filter", style = "width: 100%;", class = "button-action button-pill", icon("plus")))
)
)
,
tags$div(class = "clearBoth")
,
hr(),
wellPanel(h4(strong("Genes that match Regex")),
htmlOutput("filteredGenesFound")
,
tags$div(class = "clearBoth")
),
tags$div(class = "clearBoth")
)
),
column(5,
wellPanel(style = "background-color:lightblue;",
h4(strong("Filter Expressions")),
selectizeInput("filterExpressions", label="",
choices=NULL,
multiple=TRUE)
)
),
tags$div(class = "clearBoth")
),
tags$div(class = "BoxArea2",
h4(strong("2) Select Specific Genes:")),
wellPanel(style = "background-color:lightblue;",
textInput("customGenesLabel", "Label (no spaces)",
placeholder = "Eg. mito.genes"),
selectizeInput("filterSpecGenes", label="Select Genes",
choices=NULL,
multiple=TRUE,
options = list(
placeholder =
'Start typing gene name'
))
)
)
,
tags$div(class = "BoxArea2",
h4(strong("3) Copy/Paste Specific Genes:")),
column(8,
wellPanel(
textAreaInput("listPasteGenes", "Paste List Of Genes", width = "100%", rows = 5),
column(4,
textInput("pasteGenesLabel", "Label (no spaces)",placeholder = "Eg. ribosomal")
)
,
column(4,
selectInput("delimeter", "Delimeter",
choices = c("(comma)" = ",",
"(space)" = " ",
"(tab)" = "\t",
"(enter)" = "\n")
, selected = ",")
),
column(4,
actionButton("addFilterPaste","Add genes",class = "button button-3d button-primary", style = "width: 100%")
),
div(style = "clear:both;")
)
),
column(4,
selectizeInput("filterPasteGenes", label="Added Genes",
choices=NULL,
multiple=TRUE
),
conditionalPanel("output.genesNotFound",
tags$div(
style = "padding:10px;border: 3px solid; border-color:red; border-radius:10px; background-color:#fdfdfd; opacity: 0.90;",
h4("Genes not found"),
verbatimTextOutput("value"),
HTML("<i class=\"fa fa-info-circle\"> <small>Remove/Correct those genes that are not found and click \"Add Genes\"</small></i> "),
div(style = "clear:both;")
)
)
),
hr(),
div(style = "clear:both;")
)
,
tags$div(class = "clearBoth")
)
)
,
column(12,
actionButton("submit_data","Submit Data",class = "button button-3d button-block button-pill button-primary button-large", style = "width: 100%"))
,
tags$div(class = "clearBoth")
)
)
)
)
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