Package 'shinyMolBio' reference manual

Title:	Molecular Biology Visualization Tools for 'Shiny' Apps
Description:	Interactive visualization of 'RDML' files via 'shiny' apps. Package provides (1) PCR plate interface with ability to select individual tubes; (2) amplification/melting plots with fast hiding and highlighting individual curves; (3) 2D allelic discrimination plot.
Authors:	Konstantin A. Blagodatskikh [cre, aut]
Maintainer:	Konstantin A. Blagodatskikh <[email protected]>
License:	MIT + file LICENSE
Version:	0.6
Built:	2024-11-05 12:37:05 UTC
Source:	https://github.com/pcruniversum/shinymolbio

Create a PCR plate input control

Description

Create an input control for representing PCR plate and dynamically selecting wells inside it.

Usage

pcrPlateInput(inputId,
       label = NULL,
       plateDescription,
       pcrFormat = pcrFormatType$new(8, 12, labelFormatType$new("ABC"),
        labelFormatType$new("123")),
       selection = NULL,
       highlighting = NULL,
       wellLabelTemplate = "{{sample}}",
       onHoverWellTextTemplate = "{{position}}\u000A{{sample}}\u000A{{targets}}",
       wellClassTemplate = NULL,
       wellStyleTemplate = NULL,
       wellGroupTemplate = "{{sample}}-{{targets}}",
       cssFile = system.file("/css/pcrPlateInputStyle.css",
                 package = "shinyMolBio"),
       cssText = NULL,
       legend = NULL,
       interactive = TRUE)
pcrPlateInput(inputId,
       label = NULL,
       plateDescription,
       pcrFormat = pcrFormatType$new(8, 12, labelFormatType$new("ABC"),
        labelFormatType$new("123")),
       selection = NULL,
       highlighting = NULL,
       wellLabelTemplate = "{{sample}}",
       onHoverWellTextTemplate = "{{position}}\u000A{{sample}}\u000A{{targets}}",
       wellClassTemplate = NULL,
       wellStyleTemplate = NULL,
       wellGroupTemplate = "{{sample}}-{{targets}}",
       cssFile = system.file("/css/pcrPlateInputStyle.css",
                 package = "shinyMolBio"),
       cssText = NULL,
       legend = NULL,
       interactive = TRUE)

Arguments

`inputId`	The `input` slot that will be used to access the selected wells positions.
`label`	Display label for the control, or `NULL` for no label.
`plateDescription`	Plate description - basicly output from `RDML AsTable()` function.
`pcrFormat`	PCR plate parametrs. Should be `pcrFormatType`.
`selection`	Set preselected wells (e.g. `c("A01", "A02")` or `c(1, 2)`)
`highlighting`	Set highlighted wells (e.g. `c("A01", "A02")` or `c(1, 2)`)
`wellLabelTemplate`	Template of the well label.
`onHoverWellTextTemplate`	Template of the text on hover.
`wellClassTemplate`	Template of the well class (css class).
`wellStyleTemplate`	Template of the well style (css).
`wellGroupTemplate`	Template of the well group for selecting.
`cssFile`	Path to the css styles file.
`cssText`	CSS styles as text.
`legend`	Plate legend (any HTML content).
`interactive`	Should be this `pcrPlate` interactive or not.

Value

A PCR plate control that can be added to a UI definition.

Author(s)

Konstantin A. Blagodatskikh <[email protected]>

Examples

## Only run examples in interactive R sessions
library(RDML)
if (interactive()) {
ui <- fluidPage(
    pcrPlateInput("plate1",
                   "Plate 1",
                   RDML$new(system.file("/extdata/stepone_std.rdml", package = "RDML"))$AsTable(),
                  pcrFormatType$new(8,12,labelFormatType$new("ABC"),
                                         labelFormatType$new("123"))),
   verbatimTextOutput("selected")
 )
 server <- function(input, output) {
   output$selected <- renderText({ input$plate1 })
 }
 shinyApp(ui, server)
}
## Only run examples in interactive R sessions
library(RDML)
if (interactive()) {
ui <- fluidPage(
    pcrPlateInput("plate1",
                   "Plate 1",
                   RDML$new(system.file("/extdata/stepone_std.rdml", package = "RDML"))$AsTable(),
                  pcrFormatType$new(8,12,labelFormatType$new("ABC"),
                                         labelFormatType$new("123"))),
   verbatimTextOutput("selected")
 )
 server <- function(input, output) {
   output$selected <- renderText({ input$plate1 })
 }
 shinyApp(ui, server)
}

Printing adPlot

Description

Print a adPlot

Usage

## S3 method for class 'adPlot'
print(x)
## S3 method for class 'adPlot'
print(x)

Arguments

`x`	object of class `adPlot`

Author(s)

Konstantin A. Blagodatskikh <[email protected]>

Printing pcrCurves

Description

Print a pcrCurves

Usage

## S3 method for class 'pcrCurves'
print(x)
## S3 method for class 'pcrCurves'
print(x)

Arguments

`x`	object of class `pcrCurves`

Author(s)

Konstantin A. Blagodatskikh <[email protected]>

Examples

library(RDML)
rdml <- RDML$new(system.file("/extdata/test.rdml", package = "shinyMolBio"))
curves <- renderMeltCurves("curves1", meltCurves = rdml$GetFData(dp.type = "mdp",
 long.table = TRUE))
curves
library(RDML)
rdml <- RDML$new(system.file("/extdata/test.rdml", package = "shinyMolBio"))
curves <- renderMeltCurves("curves1", meltCurves = rdml$GetFData(dp.type = "mdp",
 long.table = TRUE))
curves

Printing PCR plate input control

Description

Print a pcrPlate

Usage

## S3 method for class 'pcrPlate'
print(x)
## S3 method for class 'pcrPlate'
print(x)

Arguments

`x`	object of class `pcrPlate`

Author(s)

Konstantin A. Blagodatskikh <[email protected]>

Renders an allelic discrimination viewer

Description

Renders a reactive allelic discrimination plot that is suitable for assigning to an UI output slot.

Usage

renderADplot(inputId, label = NULL, adData,
        targetColumn = "target.dyeId", xAxisTarget = "FAM",
        yAxisTarget = "HEX", valueColumn = "endPointRFU",
        colorBy = "genotype", polar = FALSE, showLegend = FALSE,
        plotlyCode = NULL, cssFile = NULL, cssText = NULL,
        interactive = TRUE)
renderADplot(inputId, label = NULL, adData,
        targetColumn = "target.dyeId", xAxisTarget = "FAM",
        yAxisTarget = "HEX", valueColumn = "endPointRFU",
        colorBy = "genotype", polar = FALSE, showLegend = FALSE,
        plotlyCode = NULL, cssFile = NULL, cssText = NULL,
        interactive = TRUE)

Arguments

`inputId`	The `input` slot that will be used to modify plot.
`label`	Display label for the control, or `NULL` for no label.
`adData`	Allelic descrimination data with `RDML$AsTable()` format.
`targetColumn`	Column name that contains axis splitting (dye or target).
`xAxisTarget`	X axis target (dye) name.
`yAxisTarget`	X axis target (dye) name.
`valueColumn`	Column name that contains discrimination value (RFU or cq).
`colorBy`	Column name that contains color levels data.
`polar`	Enables polar coordinates.
`showLegend`	Show plot legend.
`plotlyCode`	Your quoted custom plotly code.
`cssFile`	Path to the css styles file.
`cssText`	CSS styles as text.
`interactive`	Should be this `adPLot` interactive or not.

Author(s)

Konstantin A. Blagodatskikh <[email protected]>

Examples

library(RDML)
rdml <- RDML$new(system.file("/extdata/test.rdml", package = "shinyMolBio"))
tbl <- rdml$AsTable(endPointRFU = mean(tail(data$adp$fpoints$fluor, 5)))
tbl <- group_by(tbl, position)
tbl <- mutate(tbl,
              genotype = paste(
                if (endPointRFU[1] > 400 && endPointRFU[2] > 400) "AG"
                else if (endPointRFU[1] > 400) "AA"
                else if (endPointRFU[2] > 400) "GG"
                else "NA"
              ))
renderADplot("f", "aa", tbl, polar = TRUE, showLegend = TRUE)
library(RDML)
rdml <- RDML$new(system.file("/extdata/test.rdml", package = "shinyMolBio"))
tbl <- rdml$AsTable(endPointRFU = mean(tail(data$adp$fpoints$fluor, 5)))
tbl <- group_by(tbl, position)
tbl <- mutate(tbl,
              genotype = paste(
                if (endPointRFU[1] > 400 && endPointRFU[2] > 400) "AG"
                else if (endPointRFU[1] > 400) "AA"
                else if (endPointRFU[2] > 400) "GG"
                else "NA"
              ))
renderADplot("f", "aa", tbl, polar = TRUE, showLegend = TRUE)

Renders an amplification curves viewer

Description

Renders a reactive PCR amplification plot that is suitable for assigning to an UI output slot.

Usage

renderAmpCurves(inputId, label = NULL, ampCurves, colorBy = NULL,
  linetypeBy = NULL, logScale = FALSE, showCq = FALSE, showLegend = FALSE,
  thBy = NULL, plotlyCode = NULL, cssFile = NULL, cssText = NULL,
  interactive = TRUE)
renderAmpCurves(inputId, label = NULL, ampCurves, colorBy = NULL,
  linetypeBy = NULL, logScale = FALSE, showCq = FALSE, showLegend = FALSE,
  thBy = NULL, plotlyCode = NULL, cssFile = NULL, cssText = NULL,
  interactive = TRUE)

Arguments

`inputId`	The `input` slot that will be used to modify plot.
`label`	Display label for the control, or `NULL` for no label.
`ampCurves`	Amplification curves data with `RDML$GetFData(long.table = TRUE)` format. Columns `hideCurve` and `highlightCurve` defines which curve will be hidden or highlighted respectively.
`colorBy`	Column name that contains color levels data.
`linetypeBy`	Column name that contains linetype levels data.
`logScale`	Converts plot to `log(RFU)`.
`showCq`	Shows Cq with dots (`cq` and `quantFluor` columns have to be provided!).
`showLegend`	Show plot legend.
`thBy`	Column name that separates threshold values (`quantFluor` column have to be provided!).
`plotlyCode`	Your quoted custom plotly code.
`cssFile`	Path to the css styles file.
`cssText`	CSS styles as text.
`interactive`	Should be this `pcrPlate` interactive or not.

Author(s)

Konstantin A. Blagodatskikh <[email protected]>

Examples

library(RDML)
rdml <- RDML$new(system.file("/extdata/test.rdml", package = "shinyMolBio"))
curves <- renderAmpCurves("curves1", ampCurves = rdml$GetFData(long.table = TRUE))
curves
library(RDML)
rdml <- RDML$new(system.file("/extdata/test.rdml", package = "shinyMolBio"))
curves <- renderAmpCurves("curves1", ampCurves = rdml$GetFData(long.table = TRUE))
curves

Renders a melting curves viewer

Description

Renders a reactive melting plot that is suitable for assigning to an UI output slot.

Usage

renderMeltCurves(inputId, label = NULL, meltCurves,
  fluorColumn = "fluor", colorBy = NULL, linetypeBy = NULL, showTm = FALSE,
  showLegend = FALSE, plotlyCode = NULL, cssFile = NULL, cssText = NULL,
  interactive = TRUE)
renderMeltCurves(inputId, label = NULL, meltCurves,
  fluorColumn = "fluor", colorBy = NULL, linetypeBy = NULL, showTm = FALSE,
  showLegend = FALSE, plotlyCode = NULL, cssFile = NULL, cssText = NULL,
  interactive = TRUE)

Arguments

`inputId`	The `input` slot that will be used to modify plot.
`label`	Display label for the control, or `NULL` for no label.
`meltCurves`	Melting curves data with `RDML$GetFData(dp.type = "mdp", long.table = TRUE)` format. Columns `hideCurve` and `highlightCurve` defines which curve will be hidden or highlighted respectively.
`fluorColumn`	Column name that contains fluorescence values (can be `diffFluor` for derivative curves).
`colorBy`	Column name that contains color levels data.
`linetypeBy`	Column name that contains linetype levels data.
`showTm`	Shows Tm with dots (`tm` and `quantFluor` columns have to be provided!)
`showLegend`	Show plot legend.
`plotlyCode`	Your quoted custom plotly code.
`cssFile`	Path to the css styles file.
`cssText`	CSS styles as text.
`interactive`	Should be this `pcrPlate` interactive or not.

Author(s)

Konstantin A. Blagodatskikh <[email protected]>

Examples

library(RDML)
rdml <- RDML$new(system.file("/extdata/test.rdml", package = "shinyMolBio"))
curves <- renderMeltCurves("curves1", meltCurves = rdml$GetFData(dp.type = "mdp",
 long.table = TRUE))
curves
library(RDML)
rdml <- RDML$new(system.file("/extdata/test.rdml", package = "shinyMolBio"))
curves <- renderMeltCurves("curves1", meltCurves = rdml$GetFData(dp.type = "mdp",
 long.table = TRUE))
curves

Run shinyMolBio Example Applications

Description

Launch shinyMolBio example applications

Usage

runExample(example)
runExample(example)

Arguments

example

The name of the example to run, or NA (the default) to list the available examples.

Author(s)

Konstantin A. Blagodatskikh <[email protected]>

Examples

## Only run this example in interactive R sessions
if (interactive()) {
 # List all available examples
 runExample()

 # Run one of the examples
 runExample("pcrPlateInput")

 # Print the directory containing the code for all examples
 system.file("shiny-examples", package="shinyMolBio")
}
## Only run this example in interactive R sessions
if (interactive()) {
 # List all available examples
 runExample()

 # Run one of the examples
 runExample("pcrPlateInput")

 # Print the directory containing the code for all examples
 system.file("shiny-examples", package="shinyMolBio")
}

Change the value of a render ADplot control on the client

Description

Change the value of a render ADplot control on the client

Usage

updateADplot(
  session,
  inputId,
  label = NULL,
  hidePoints = NULL,
  highlightPoints = NULL
)
updateADplot(
  session,
  inputId,
  label = NULL,
  hidePoints = NULL,
  highlightPoints = NULL
)

Arguments

`session`	The `session` object passed to function given to `shinyServer`.
`inputId`	The id of the `input` object.
`label`	The label to set for the input object.
`hidePoints`	The `position` of the points to be hiden.
`highlightPoints`	The `position` of the points to be highlighted.

Author(s)

Konstantin A. Blagodatskikh <[email protected]>

Change the value of a render PCR curves control on the client

Description

Change the value of a render PCR curves control on the client

Usage

updateCurves(
  session,
  inputId,
  label = NULL,
  hideCurves = NULL,
  highlightCurves = NULL
)
updateCurves(
  session,
  inputId,
  label = NULL,
  hideCurves = NULL,
  highlightCurves = NULL
)

Arguments

`session`	The `session` object passed to function given to `shinyServer`.
`inputId`	The id of the `input` object.
`label`	The label to set for the input object.
`hideCurves`	The `fdata.names` of the curves to be hiden.
`highlightCurves`	The `fdata.names` of the curves to be highlighted.

Author(s)

Konstantin A. Blagodatskikh <[email protected]>

Change the value of a PCR plate input control on the client

Description

Change the value of a PCR plate input control on the client

Usage

updatePcrPlateInput(
  session,
  inputId,
  label = NULL,
  selection = NULL,
  highlighting = NULL
)
updatePcrPlateInput(
  session,
  inputId,
  label = NULL,
  selection = NULL,
  highlighting = NULL
)

Arguments

`session`	The `session` object passed to function given to `shinyServer`.
`inputId`	The id of the `input` object.
`label`	The label to set for the input object.
`selection`	The positions of the wells to be selected.
`highlighting`	The positions of the wells to be highlighted.

Author(s)

Konstantin A. Blagodatskikh <[email protected]>

Examples

## Only run examples in interactive R sessions
library(RDML)
if (interactive()) {
ui <- fluidPage(
    pcrPlateInput("plate1",
                   "Plate 1",
                   RDML$new(system.file("/extdata/stepone_std.rdml", package = "RDML"))$AsTable(),
                  pcrFormatType$new(8,12,labelFormatType$new("ABC"),
                                         labelFormatType$new("123"))),
   verbatimTextOutput("selected"),
   actionButton("selectWellBtn",
                "Select Well A01-A03")
 )
 server <- function(input, output, session) {
   output$selected <- renderText({ input$plate1 })

   observeEvent(
               input$selectWellBtn,
               {
           updatePcrPlateInput(session,
           "plate1",
           selection = c("A01", "A02", "A03"))
  })
 }
 shinyApp(ui, server)
}
## Only run examples in interactive R sessions
library(RDML)
if (interactive()) {
ui <- fluidPage(
    pcrPlateInput("plate1",
                   "Plate 1",
                   RDML$new(system.file("/extdata/stepone_std.rdml", package = "RDML"))$AsTable(),
                  pcrFormatType$new(8,12,labelFormatType$new("ABC"),
                                         labelFormatType$new("123"))),
   verbatimTextOutput("selected"),
   actionButton("selectWellBtn",
                "Select Well A01-A03")
 )
 server <- function(input, output, session) {
   output$selected <- renderText({ input$plate1 })

   observeEvent(
               input$selectWellBtn,
               {
           updatePcrPlateInput(session,
           "plate1",
           selection = c("A01", "A02", "A03"))
  })
 }
 shinyApp(ui, server)
}

Package 'shinyMolBio'

Help Index

Create a PCR plate input control

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Printing adPlot

Description

Usage

Arguments

Author(s)

See Also

Printing pcrCurves

Description

Usage

Arguments

Author(s)

See Also

Examples

Printing PCR plate input control

Description

Usage

Arguments

Author(s)

See Also

Renders an allelic discrimination viewer

Description

Usage

Arguments

Author(s)

See Also

Examples

Renders an amplification curves viewer

Description

Usage

Arguments

Author(s)

See Also

Examples

Renders a melting curves viewer

Description

Usage

Arguments

Author(s)

See Also

Examples

Run shinyMolBio Example Applications

Description

Usage

Arguments

Author(s)

Examples

Change the value of a render ADplot control on the client

Description

Usage

Arguments

Author(s)

Change the value of a render PCR curves control on the client

Description

Usage

Arguments

Author(s)

Change the value of a PCR plate input control on the client

Description

Usage

Arguments

Author(s)

Examples