Type: Package
Title: Web-Based Interactive Omics Visualization
Version: 2.4.2
Description: Tool-set of modules for creating web-based applications that use plot based strategies to visualize and analyze multi-omics data. This package utilizes the 'shiny' and 'plotly' frameworks to provide a user friendly dashboard for interactive plotting.
URL: https://github.com/loosolab/wilson/
BugReports: https://github.com/loosolab/wilson/issues/
License: MIT + file LICENSE
Encoding: UTF-8
Imports: shiny, data.table, ggplot2, plotly (> 4.8.0), scales, shinydashboard, DT (≥ 0.3), colourpicker, RColorBrewer, shinyjs, viridis, rje, grDevices, grid, plyr, circlize, ComplexHeatmap, stats, gplots, reshape, rintrojs, RJSONIO, ggrepel (≥ 0.6.12), DESeq2, rjson, FactoMineR, factoextra, heatmaply (≥ 0.14.1), shinycssloaders, log4r, openssl, methods, R6, zip, shinyWidgets
RoxygenNote: 7.1.1
Suggests: knitr, rmarkdown, testthat, stringi, utils
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-04-19 09:17:56 UTC; hschult
Author: Hendrik Schultheis [aut, cre], Jens Preussner [aut], Looso Mario [aut]
Maintainer: Hendrik Schultheis <hendrik.schultheis@mpi-bn.mpg.de>
Repository: CRAN
Date/Publication: 2021-04-19 09:40:02 UTC

Clarion R6-class definition

Description

Use this to create a clarion object. This object is used by all top-level wilson modules.

Constructor

Clarion$new(header = NULL, metadata, data, validate = TRUE)

Constructor Arguments

Variable Return
header A named list. Defaults to NULL.
metadata Clarion metadata in form of a data.table.
data Data.table according to metadata.
validate Logical value to validate on initialization. Defaults to TRUE.

Public fields

header

List of global information regarding the whole experiment.

metadata

Data.table with additional information for each column.

data

Data.table containing experiment result data.

Methods

Public methods

Method get_id()

Returns name of unique identifier column. Assumes first feature to be unique if not specified.

Usage
Clarion$get_id()
Returns

Name of the id column.

Method get_name()

Returns name of name column. If not specified return unique Id.

Usage
Clarion$get_name()
Returns

Name of the name column.

Method get_delimiter()

Return delimiter used within multi-value fields (no delimiter = NULL).

Usage
Clarion$get_delimiter()

Method is_delimited()

Logical whether the given column name is delimited.

Usage
Clarion$is_delimited(x)
Arguments
x

Name of the column.

Returns

boolean

Method get_factors()

Get factors to all columns.

Usage
Clarion$get_factors()
Details

Named factors (e.g. factor1="name") will be cropped to their name.

Returns

Returns a data.table columns: key and factor(s) if any.

Method get_level()

Get level(s) to given column name(s).

Usage
Clarion$get_level(column)
Arguments
column

One or more column name(s).

Returns

Provide a vector of levels to the given columnnames in column. Returns NA for missing columns and character(0) if column = NULL.

Method get_label()

Get label(s) to given column name(s).

Usage
Clarion$get_label(column = NULL, sub_label = TRUE, sep = " ")
Arguments
column

One or more column name(s).

sub_label

Whether the sub_label should be included.

sep

Separator between label and sub_label.

Details

If a column does not have a label the key is returned.

Returns

Provides a vector of labels (+ sub_label) to the given columnnames in column. Returns NA for missing columns and all labels if column = NULL.

Method validate()

Check the object for inconsistencies.

Usage
Clarion$validate(solve = TRUE)
Arguments
solve

For solve = TRUE try to resolve some warnings.

Method new()

Initialize a new clarion object.

Usage
Clarion$new(header = NULL, metadata, data, validate = TRUE)
Arguments
header

A named list. Defaults to NULL.

metadata

Clarion metadata in form of a data.table.

data

Data.table according to metadata.

validate

Logical value to validate on initialization. Defaults to TRUE.

Returns

Clarion object.

Method write()

Save the object as a clarion file.

Usage
Clarion$write(file)
Arguments
file

Filename for the file to be written.

Method clone()

The objects of this class are cloneable with this method.

Usage
Clarion$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

## Not run: 
# initializing a new object
object <- Clarion$new(header, metadata, data, validate = TRUE)

# create a deep copy
object_copy <- object$clone(deep = TRUE)

## End(Not run)

AND module server logic

Description

This function evaluates output from multiple OR modules by combining with a logical and.

Usage

and(
  input,
  output,
  session,
  data,
  show.elements = NULL,
  element.grouping = NULL,
  column.labels = NULL,
  delimiter = NULL,
  multiple = TRUE,
  contains = FALSE,
  ranged = FALSE,
  step = 100,
  reset = NULL
)

Arguments

input

Shiny's input object.

output

Shiny's output object.

session

Shiny's session object.

data

The input data.frame for which selection should be provided. Evaluates an OR module for each column (Supports reactive).

show.elements

A Vector of column names determining which OR modules are shown. Defaults to names(data). (Supports reactive)

element.grouping

Group features in boxes. (Data.table: first column = columnnames, second column = groupnames) (Supports reactive)

column.labels

Additional labels for the columns, defaults to names(data).

delimiter

A single character, or a vector indicating how column values are delimited. (Fills vector sequentially if needed)(Supports reactive)

multiple

Whether or not textual ORs should allow multiple selections. (Fills vector sequentially if needed)(Supports reactive)

contains

Whether or not textual ORs are initialized as textInput checking entries for given string. (Fills vector sequentially if needed)(Supports reactive)

ranged

Whether or not numeric ORs are ranged. (Fills vector sequentially if needed)(Supports reactive)

step

Set numeric ORs slider steps. (Fills vector sequentially if needed)(Supports reactive)

reset

Reactive which will cause a UI reset on change.

Value

A reactive containing named list with a boolean vector of length nrow(data) (bool), indicating whether an observation is selected or not and a vector of Strings showing the used filter (text).

AND module UI representation

Description

The AND module connects filtering and selection across multiple columns of a data.frame. Columns of class boolean, character or factor will be represented as textual ORs, numeric columns as numerical OR.

Usage

andUI(id)

Arguments

id

The ID of the modules namespace.

Value

A list with HTML tags from tag.

Function to generate categorical (qualitative) color palettes

Description

Function to generate categorical (qualitative) color palettes

Usage

categoricalPalettes(n)

Arguments

n

Number of colors to generate

Value

A data.table with (named) color palettes of length n

colorPicker module server logic

Description

Provides server logic for the colorPicker2 module.

Usage

colorPicker(
  input,
  output,
  session,
  num.colors = 256,
  distribution = "all",
  winsorize = NULL,
  selected = NULL
)

Arguments

input

Shiny's input object

output

Shiny's output object

session

Shiny's session object

num.colors

Define length of colorpalette vector (Default = 256).

distribution

Decide which palettes are selectable. One or more of list("sequential", "diverging", "categorical"). Defaults to "all" (Supports reactive).

winsorize

Numeric vector of two. Dynamically change lower and upper limit (supports reactive). Defaults to NULL.

selected

Set the default selected palette.

Details

A custom colorpalette's return will be NULL if there is something wrong with it.

equalize will be returned as FALSE if not selected.

Value

Reactive containing list(palette = c(colors), name = palette_name, transparency = Integer, reverse = Boolean, winsorize = NULL or a two-component vector containing lower and upper limits).

colorPicker module UI representation

Description

The functions creates HTML tag definitions of its representation based on the parameters supplied. Currently, two UI can be created for the user to choose either (a) colors from a given color scheme, or (b) choose one or more single colors.

Usage

colorPickerUI(
  id,
  label = "Color scheme",
  custom = FALSE,
  multiple = FALSE,
  show.reverse = TRUE,
  show.scaleoptions = TRUE,
  show.transparency = TRUE
)

Arguments

id

The ID of the modules namespace.

label

Either a character vector of length one with the label for the color scheme dropdown, or a character vector containing labels of the single colors.

custom

Boolean if TRUE custom colors can be selected (Default = FALSE).

multiple

Boolean value, if set to TRUE custom colorpalettes can be made. Only if custom = TRUE (Default = FALSE).

show.reverse

Logical, whether or not to show the reverse switch (Default = TRUE).

show.scaleoptions

Logical, whether or not to show color scaling option winsorize (Default = TRUE).

show.transparency

Logical, whether or not to show the transparency slider (Default = TRUE).

Value

A list with HTML tags from tag.

columnSelector module server logic

Description

columnSelector module server logic

Usage

columnSelector(
  input,
  output,
  session,
  type.columns,
  type = NULL,
  column.type.label = "Type of Column",
  label.label = "Label",
  multiple = TRUE,
  none = FALSE,
  sep = ", ",
  suffix = NULL
)

Arguments

input

Shiny's input object

output

Shiny's output object

session

Shiny's session object

type.columns

data.table: (Supports reactive) key = columnnames (id) level = datalevel/ type of column label = optional, used instead of id sub_label = optional, added to id/ label

type

The type (contrast/group/sample of the type dropdown menu, selected in step 1 (upper dropdown). Defaults to unique(type.columns[,2]) (Supports reactive)

column.type.label

Changes the label of the first UI element

label.label

Change label above label text input.

multiple

Boolean value whether multiple values can be selected in second selector. (Default = TRUE)

none

If TRUE adds "None to secondSelector and select is. (Default = FALSE)

sep

Used to separate labels on multi value selection.

suffix

Added to label only on multiple = FALSE (supports reactive). Also uses sep as separator.

Value

Returns the input. As named list: names("type", "selected_columns", "label")

columnSelector module UI representation

Description

columnSelector module UI representation

Usage

columnSelectorUI(id, label = FALSE, title = NULL)

Arguments

id

The ID of the modules namespace.

label

Boolean value; if true include a text input field with the desired axis label (this should be preset with the headline of the column)

title

String which is displayed as module title. (Default = NULL)

Value

A list from tag with the UI elements.

Method for geneView creation

Description

Method for geneView creation

Usage

create_geneview(
  data,
  grouping,
  plot.type = "line",
  facet.target = "gene",
  facet.cols = 2,
  colors = NULL,
  ylabel = NULL,
  ylimits = NULL,
  gene.label = NULL,
  plot.method = "static",
  width = "auto",
  height = "auto",
  ppi = 72,
  scale = 1
)

Arguments

data

data.table containing plot data

grouping

data.table metadata containing: column1 : key column2 : factor1

plot.type

String specifying which plot type is used c("box", "line", "violin", "bar").

facet.target

Target to plot on x-Axis c("gene", "condition").

facet.cols

Number of plots per row.

colors

Vector of colors used for color palette

ylabel

Label of the y-axis (default = NULL).

ylimits

Vector defining scale of y-axis (default = NULL).

gene.label

Vector of labels used instead of gene names (default = NULL).

plot.method

Choose which method used for plotting. Either "static" or "interactive" (Default = "static").

width

Set the width of the plot in cm (default = "auto").

height

Set the height of the plot in cm (default = "auto").

ppi

Pixel per inch (default = 72).

scale

Modify plot size while preserving aspect ratio (Default = 1).

Details

Width/ height limit = 500. If exceeded default to 500 and issue exceed_size = TRUE.

Value

Returns depending on plot.method list(plot = ggplot/ plotly object, width = width in cm, height = height in cm, ppi = pixel per inch, exceed_size = Boolean).

Method for heatmap creation

Description

Method for heatmap creation

Usage

create_heatmap(
  data,
  unitlabel = "auto",
  row.label = TRUE,
  row.custom.label = NULL,
  column.label = TRUE,
  column.custom.label = NULL,
  clustering = "none",
  clustdist = "auto",
  clustmethod = "auto",
  colors = NULL,
  winsorize.colors = NULL,
  plot.method = "static",
  width = "auto",
  height = "auto",
  ppi = 72,
  scale = 1
)

Arguments

data

data.table containing plot data. First column contains row labels.

unitlabel

label of the colorbar

row.label

Logical whether or not to show row labels.

row.custom.label

Vector of custom row labels.

column.label

Logical whether or not to show column labels.

column.custom.label

Vector of custom column labels.

clustering

How to apply clustering on data. c("none", "both", "column", "row")

clustdist

Which cluster distance to use. See heatmapr.

clustmethod

Which cluster method to use. See heatmapr.

colors

Vector of colors used for color palette.

winsorize.colors

NULL or a vector of length two, giving the values of colorbar ends (default = NULL).

plot.method

Choose which method is used for plotting. Either "plotly" or "complexHeatmap" (Default = "complexHeatmap").

width

Set width of plot in cm (Default = "auto").

height

Set height of plot in cm (Default = "auto").

ppi

Pixel per inch (default = 72).

scale

Modify plot size while preserving aspect ratio (Default = 1).

Details

Width/ height limit = 500. If exceeded default to 500 and issue exceed_size = TRUE.

Value

Returns list(plot = complexHeatmap/ plotly object, width = width in cm, height = height in cm, ppi = pixel per inch, exceed_size = Boolean whether width/ height exceeded max) depending on plot.method.

Method for pca creation.

Description

Method for pca creation.

Usage

create_pca(
  data,
  color.group = NULL,
  color.title = NULL,
  palette = NULL,
  shape.group = NULL,
  shape.title = NULL,
  shapes = c(15:25),
  dimension.a = 1,
  dimension.b = 2,
  dimensions = 6,
  on.columns = TRUE,
  labels = FALSE,
  custom.labels = NULL,
  pointsize = 2,
  labelsize = 3,
  width = 28,
  height = 28,
  ppi = 72,
  scale = 1
)

Arguments

data

data.table from which the plot is created (First column will be handled as rownames if not numeric).

color.group

Vector of groups according to samples (= column names).

color.title

Title of the color legend.

palette

Vector of colors used for color palette.

shape.group

Vector of groups according to samples (= column names).

shape.title

Title of the shape legend.

shapes

Vector of shapes see points. Will recycle/ cut off shapes if needed. Default = c(15:25)

dimension.a

Number of dimension displayed on X-Axis.

dimension.b

Number of dimension displayed on Y-Axis.

dimensions

Number of dimensions to create.

on.columns

Boolean perform pca on columns or rows.

labels

Boolean show labels.

custom.labels

Vector of custom labels. Will replace columnnames.

pointsize

Size of the data points.

labelsize

Size of texts inside plot (default = 3).

width

Set the width of the plot in cm (default = 28).

height

Set the height of the plot in cm (default = 28).

ppi

Pixel per inch (default = 72).

scale

Modify plot size while preserving aspect ratio (Default = 1).

Details

If width and height are the same axis ratio will be set to one (quadratic plot).

Width/ height limit = 500. If exceeded default to 500 and issue exceed_size = TRUE.

Value

A named list(plot = ggplot object, data = pca.data, width = width of plot (cm), height = height of plot (cm), ppi = pixel per inch, exceed_size = Boolean whether width/ height exceeded max).

Method for scatter plot creation

Description

Method for scatter plot creation

Usage

create_scatterplot(
  data,
  data.labels = NULL,
  data.hovertext = NULL,
  transparency = 1,
  pointsize = 1,
  labelsize = 3,
  color = NULL,
  x_label = "",
  y_label = "",
  z_label = "",
  density = TRUE,
  line = TRUE,
  categorized = FALSE,
  highlight.data = NULL,
  highlight.labels = NULL,
  highlight.hovertext = NULL,
  highlight.color = "#FF0000",
  xlim = NULL,
  ylim = NULL,
  colorbar.limits = NULL,
  width = "auto",
  height = "auto",
  ppi = 72,
  plot.method = "static",
  scale = 1
)

Arguments

data

data.table containing plot data column 1: id column 2, 3(, 4): x, y(, z)

data.labels

Vector of labels used for data. Length has to be equal to nrow(data).

data.hovertext

Character vector with additional hovertext. Length has to be equal to nrow(data).

transparency

Set point transparency. See geom_point.

pointsize

Set point size. See geom_point.

labelsize

Set label size. See geom_text.

color

Vector of colors used for color palette.

x_label

Label x-Axis

y_label

Label Y-Axis

z_label

Label Z-Axis

density

Boolean value, perform 2d density estimate.

line

Boolean value, add reference line.

categorized

Z-Axis (if exists) as categories.

highlight.data

data.table containing data to highlight. Same structure as data.

highlight.labels

Vector of labels used for highlighted data. Length has to be equal to nrow(highlight.data).

highlight.hovertext

Character vector with additional hovertext. Length has to be equal to nrow(highlight.data).

highlight.color

String with hexadecimal color-code.

xlim

Numeric vector of two setting min and max limit of x-axis. See lims.

ylim

Numeric vector of two setting min and max limit of y-axis. See lims.

colorbar.limits

Vector with min, max values for colorbar (Default = NULL).

width

Set plot width in cm (Default = "auto").

height

Set plot height in cm (Default = "auto").

ppi

Pixel per inch (default = 72).

plot.method

Whether the plot should be 'interactive' or 'static' (Default = 'static').

scale

Modify plot size while preserving aspect ratio (Default = 1).

Details

Width/ height limit = 500. If exceeded default to 500 and issue exceed_size = TRUE.

Value

Returns list(plot = ggplotly/ ggplot, width, height, ppi, exceed_size).

Function to generate diverging (two-sided) color palettes (e.g. for log2fc, zscore)

Description

Function to generate diverging (two-sided) color palettes (e.g. for log2fc, zscore)

Usage

divergingPalettes(n)

Arguments

n

Number of colors to generate

Value

A data.table with (named) color palettes of length n

Function used for downloading. Creates a zip container containing plot in png, pdf and user input in json format. Use inside downloadHandler content function.

Description

Function used for downloading. Creates a zip container containing plot in png, pdf and user input in json format. Use inside downloadHandler content function.

Usage

download(
  file,
  filename,
  plot,
  width,
  height,
  ppi = 72,
  save_plot = TRUE,
  ui = NULL
)

Arguments

file

See downloadHandler content parameter.

filename

See downloadHandler.

plot

Plot to download.

width

in centimeter.

height

in centimeter.

ppi

pixel per inch. Defaults to 72.

save_plot

Logical if plot object should be saved as .RData.

ui

List of user inputs. Will be converted to JavaScript Object Notation. See toJSON

Value

Path to zip archive invisibly. See zipr.

Method to get equalized min/max values from vector

Description

Method to get equalized min/max values from vector

Usage

equalize(values)

Arguments

values

Numeric vector or table

Value

Vector with c(min, max).

featureSelector module server logic

Description

featureSelector module server logic

Usage

featureSelector(
  input,
  output,
  session,
  clarion,
  multiple = TRUE,
  contains = FALSE,
  ranged = TRUE,
  step = 100,
  truncate = 30,
  selection.default = "all"
)

Arguments

input

Shiny's input object.

output

Shiny's output object.

session

Shiny's session object.

clarion

A clarion object. See Clarion. (Supports reactive)

multiple

Whether or not textual ORs should allow multiple selections. (Fills vector sequentially if needed)(Supports reactive)

contains

Whether or not textual ORs are initialized as textInput checking entries for given string. (Fills vector sequentially if needed)(Supports reactive)

ranged

Whether or not numeric ORs are ranged. (Fills vector sequentially if needed)(Supports reactive)

step

Set numeric ORs number of slider steps. (Fills vector sequentially if needed)(Supports reactive)

truncate

Truncate datatable entries at x characters (Default = 30).

selection.default

Decide whether everything or nothing is selected on default (no filters applied). Either "all" or "none" (Default = "all").

Details

Keep in mind that the order of features (columns in clarion$data) is the order in which multiple, contains, ranged and step are evaluated.

Value

Reactive containing names list: Selected data as reactive containing clarion object (object). Used filter to select data (filter).

featureSelector module guide

Description

featureSelector module guide

Usage

featureSelectorGuide(session)

Arguments

session

The shiny session

Value

A shiny reactive that contains the texts for the guide steps.

featureSelector module UI representation

Description

featureSelector module UI representation

Usage

featureSelectorUI(id)

Arguments

id

The ID of the modules namespace

Value

A list with HTML tags from tag

Force evaluation of the parent function's arguments.

Description

Force evaluation of the parent function's arguments.

Usage

forceArgs(args)

Arguments

args

List of Argument names to force evaluation. Defaults to all named arguments see match.call.

Details

Similar to forceAndCall but used from within the respective function.

This method is not using force as it is restricted to it's calling environment. Instead get is used.

geneView's module server logic

Description

Provides server logic for the geneView module.

Usage

geneView(
  input,
  output,
  session,
  clarion,
  plot.method = "static",
  label.sep = ", ",
  width = "auto",
  height = "auto",
  ppi = 72,
  scale = 1
)

Arguments

input

Shiny's input object.

output

Shiny's output object.

session

Shiny's session object.

clarion

A clarion object. See Clarion. (Supports reactive)

plot.method

Choose which method is used for plotting. Either "static" or "interactive" (Default = "static").

label.sep

Separator used for label merging (Default = ", ").

width

Width of the plot in cm. Defaults to minimal size for readable labels and supports reactive.

height

Height of the plot in cm. Defaults to minimal size for readable labels and supports reactive.

ppi

Pixel per inch. Defaults to 72 and supports reactive.

scale

Scale plot size. Defaults to 1, supports reactive.

Details

Width/ height/ ppi less or equal to default will use default value.

Ppi less or equal to zero will use default.

Value

Reactive containing data.table used for plotting.

geneView module guide

Description

geneView module guide

Usage

geneViewGuide(session)

Arguments

session

The shiny session

Value

A shiny reactive that contains the texts for the Guide steps.

geneView's module UI representation

Description

geneView's module UI representation

Usage

geneViewUI(id, plot.columns = 3)

Arguments

id

The ID of the modules namespace.

plot.columns

Initial value of plot column slider. Integer value between 1 and 7 (Default = 3).

Value

A list with HTML tags from tag.

global correlation heatmap module server logic

Description

global correlation heatmap module server logic

Usage

global_cor_heatmap(
  input,
  output,
  session,
  clarion,
  plot.method = "static",
  width = "auto",
  height = "auto",
  ppi = 72,
  scale = 1
)

Arguments

input

Shiny's input object

output

Shiny's output object

session

Shiny's session object

clarion

A clarion object. See Clarion. (Supports reactive)

plot.method

Choose which method is used for plotting. Either "static" or "interactive" (Default = "static").

width

Width of the plot in cm. Defaults to minimal size for readable labels and supports reactive.

height

Height of the plot in cm. Defaults to minimal size for readable labels and supports reactive.

ppi

Pixel per inch. Defaults to 72 and supports reactive.

scale

Scale plot size. Defaults to 1, supports reactive.

Value

Reactive containing data used for plotting.

global correlation heatmap module UI representation

Description

global correlation heatmap module UI representation

Usage

global_cor_heatmapUI(id)

Arguments

id

The ID of the modules namespace.

Value

A list with HTML tags from tag

global correlation heatmap module guide

Description

global correlation heatmap module guide

Usage

global_cor_heatmap_guide(session)

Arguments

session

The shiny session

Value

A shiny reactive that contains the texts for the Guide steps.

heatmap module server logic

Description

heatmap module server logic

Usage

heatmap(
  input,
  output,
  session,
  clarion,
  plot.method = "static",
  label.sep = ", ",
  width = "auto",
  height = "auto",
  ppi = 72,
  scale = 1
)

Arguments

input

Shiny's input object

output

Shiny's output object

session

Shiny's session object

clarion

A clarion object. See Clarion. (Supports reactive)

plot.method

Choose which method is used for plotting. Either "static" or "interactive" (Default = "static").

label.sep

Separator used for label merging (Default = ", ").

width

Width of the plot in cm. Defaults to minimal size for readable labels and supports reactive.

height

Height of the plot in cm. Defaults to minimal size for readable labels and supports reactive.

ppi

Pixel per inch. Defaults to 72 and supports reactive.

scale

Scale plot size. Defaults to 1, supports reactive.

Value

Reactive containing data used for plotting.

heatmap module guide

Description

heatmap module guide

Usage

heatmapGuide(session)

Arguments

session

The shiny session

Value

A shiny reactive that contains the texts for the Guide steps.

heatmap module UI representation

Description

heatmap module UI representation

Usage

heatmapUI(id, row.label = TRUE)

Arguments

id

The ID of the modules namespace.

row.label

Boolean Value set initial Value for rowlabel checkbox (Default = TRUE).

Value

A list with HTML tags from tag.

Download and install Wilson Apps

Description

Download and install Wilson Apps

Usage

install_app(
  location = ".",
  remove_data = FALSE,
  start_after_install = FALSE,
  app_name = "wilson-basic",
  repository = "https://github.molgen.mpg.de/loosolab/wilson-apps"
)

Arguments

location

Where the app should be installed. Default is current location.

remove_data

If TRUE demo data will be deleted.

start_after_install

Start the app when done installing.

app_name

Select app to install.

repository

Link to the repository that holds the apps.

Details

Will create a folder named after parameter app_name.

label module server logic

Description

label module server logic

Usage

label(
  input,
  output,
  session,
  data,
  label = "Select label columns",
  multiple = TRUE,
  sep = ", ",
  unique = TRUE,
  unique_sep = "_",
  disable = NULL
)

Arguments

input

Shiny's input object.

output

Shiny's output object.

session

Shiny's session object.

data

Data.table used for label creation. Column names will be used for selection. (supports reactive)

label

Set label of selectizeInput.

multiple

Allow multiple selection which will be merged with sep (default = TRUE).

sep

Separator used to collapse selection (default = ", ").

unique

Make labels unique. Defaults to TRUE. See make.unique.

unique_sep

Separator used for unique (default = "_"). Should differ from sep.

disable

Reactive containing boolean. To disable/ enable module.

Value

Reactive containing list(label = vector of strings or NULL on empty selection, selected = user input).

label module UI representation

Description

label module UI representation

Usage

labelUI(id)

Arguments

id

The ID of the modules namespace

Value

A list with HTML tags from tag

limit module server logic

Description

limit module server logic

Usage

limit(input, output, session, lower = NULL, upper = NULL)

Arguments

input

Shiny's input object.

output

Shiny's output object.

session

Shiny's session object.

lower

Set lower limit (supports reactive).

upper

Set upper limit (supports reactive).

Value

Reactive containing: list(lower, upper).

limit module UI representation

Description

limit module UI representation

Usage

limitUI(id, label = "Limit")

Arguments

id

The ID of the modules namespace

label

Set the modules label.

Value

A list with HTML tags from tag

logger message convenience function

Description

logger message convenience function

Usage

log_message(
  message,
  level = c("DEBUG", "INFO", "WARN", "ERROR", "FATAL"),
  token = NULL
)

Arguments

message

String of message to be written in log. See levellog.

level

Set priority level of the message (number or character). See levellog.

token

Use token bound to this identifier.

Details

Does nothing if logger doesn't exist.

marker module server logic

Description

marker module server logic

Usage

marker(input, output, session, clarion)

Arguments

input

Shiny's input object.

output

Shiny's output object.

session

Shiny's session object.

clarion

A clarion object. See Clarion. (Supports reactive)

Value

A named list containing reactives (highlight, color, labelColumn, label, clarion).

marker module UI representation

Description

marker module UI representation

Usage

markerUI(id, label = "Highlight/ Label Selected Features")

Arguments

id

The ID of the modules namespace

label

Set label of first element.

Value

A list with HTML tags from tag

orNumeric module server logic

Description

Provides server logic for the orNumeric module.

Usage

orNumeric(
  input,
  output,
  session,
  choices,
  value,
  label = "Column",
  step = 100,
  stepsize = NULL,
  min. = shiny::reactive(min(choices_r(), na.rm = TRUE)),
  max. = shiny::reactive(max(choices_r(), na.rm = TRUE)),
  label.slider = NULL,
  zoomable = TRUE,
  reset = NULL
)

Arguments

input

Shiny's input object.

output

Shiny's output object.

session

Shiny's session object.

choices

A list or a numeric vector with the possible choices offered in the UI. See sliderInput (Supports reactive).

value

Initial value of the slider. Creates a ranged slider if numeric vector of two given (Supports reactive).

label

Label of the entire module.

step

Number of steps on interval (Default = 100).

stepsize

Value defining interval size of the slider. Will be used instead of step (Default = NULL).

min.

Minimum value that can be selected on slider (defaults to min(choices)) (Supports reactive).

max.

Maximum value that can be selected on slider (defaults to max(choices)) (Supports reactive).

label.slider

A character vector of length one with the label for the sliderInput.

zoomable

Boolean to enable zooming. Redefine the sliders range. Defaults to TRUE.

reset

A reactive which will trigger a module reset on change.

Value

Returns a reactive containing a named list with the label, the selected choices as a character vector (text), a boolean vector of length length(choices) (bool), and a vector of the selected value(s) (value), indicating whether a item has been chosen. If no item has been chosen, the return is TRUE for items.

orNumeric module UI representation

Description

This module allows to select value/range inputs from a sliderInput element. The functions creates HTML tag definitions of its representation based on the parameters supplied.

Usage

orNumericUI(id)

Arguments

id

The ID of the modules namespace.

Value

A list with HTML tags from tag.

orTextual module server logic

Description

Provides server logic for the orTextual module.

Usage

orTextual(
  input,
  output,
  session,
  choices,
  selected = NULL,
  label = "Column",
  delimiter = NULL,
  multiple = TRUE,
  contains = FALSE,
  reset = NULL,
  parse_mode = TRUE
)

Arguments

input

Shiny's input object.

output

Shiny's output object.

session

Shiny's session object.

choices

A list or a character vector with the possible choices offered in the UI. See selectInput.

selected

The initially selected value. See selectInput.

label

A character vector of length one with the label for the selectInput.

delimiter

A single character indicating if and how items are delimited (default: NULL indicates no delimitation). Only if contains = FALSE.

multiple

Whether or not selection of multiple items is allowed.

contains

Logical variable. If TRUE shows module as a textsearch input.

reset

A reactive which will trigger a module reset on change.

parse_mode

Boolean to enable text to selection parsing. Ignored if multiple = FALSE or contains = TRUE.

Value

Returns a reactive containing a named list with the label, the selected choices as a character vector (text) and a boolean vector of length length(choices) (bool), indicating whether a item has been chosen. If no item has been chosen, the return is TRUE for items.

orTextual module UI representation

Description

This module allows to select (multiple) inputs from a selectInput element. The functions creates HTML tag definitions of its representation based on the parameters supplied.

Usage

orTextualUI(id)

Arguments

id

The ID of the modules namespace.

Value

A list with HTML tags from tag.

Converting MaxQuant Output file proteinGroups.txt to CLARION format by creating a headline of metadata for each column

Description

List with columns of reduced version (see config.json file) If you only want the samples of a specific keyword write: column;exp For example: You got: Intensity Intensity 'experiment_name' Do you want both add "Intensity" to the list. Do you only want the sample add "Intensity;exp" to the list Anything else like 'Intensity;ex' or 'Intensity;' results in writing both. Only works if there are samples of that type. If not, column does not show up in file

Usage

parse_MaxQuant(
  proteinGroups_in,
  summary_in,
  outfile,
  outfile_reduced,
  config = system.file("extdata", "parser_MaxQuant_config.json", package = "wilson"),
  delimiter = ";",
  format = NULL,
  version = NULL,
  experiment_id = NULL
)

Arguments

proteinGroups_in

path of proteinGroup.txt file

summary_in

path of belonging summary.txt file

outfile

path of full CLARION output file

outfile_reduced

path of reduced CLARION output file

config

path of config file (containing information about metadata)

delimiter

delimiter (Default = ;)

format

pre-header information about format (optional)

version

pre-header information about version (optional)

experiment_id

pre-header information about experiment id (optional)

Value

TRUE on success

Author(s)

Rene Wiegandt

Method to parse input file.

Description

Method to parse input file.

Usage

parser(file, dec = ".")

Arguments

file

Path to file that needs parsing.

dec

The decimal separator. See fread.

Value

Clarion object. See Clarion

pca module server logic

Description

pca module server logic

Usage

pca(
  input,
  output,
  session,
  clarion,
  width = 28,
  height = 28,
  ppi = 72,
  scale = 1
)

Arguments

input

Shiny's input object

output

Shiny's output object

session

Shiny's session object

clarion

A clarion object. See Clarion. (Supports reactive)

width

Width of the plot in cm. Defaults to 28 and supports reactive.

height

Height of the plot in cm. Defaults to 28 and supports reactive.

ppi

Pixel per inch. Defaults to 72 and supports reactive.

scale

Scale plot size. Defaults to 1, supports reactive.

Details

Width/ height/ ppi less or equal to zero will use default value.

Value

A reactive containing list with dimensions.

pca module guide

Description

pca module guide

Usage

pcaGuide(session)

Arguments

session

The shiny session

Value

A shiny reactive that contains the texts for the Guide steps.

pca module UI representation

Description

pca module UI representation

Usage

pcaUI(id, show.label = TRUE)

Arguments

id

The ID of the modules namespace.

show.label

Set initial value of show label checkbox (Default = TRUE).

Value

A list with HTML tags from tag.

Defines additional questions asked before CRAN submission. DO NOT EXPORT!

Description

Defines additional questions asked before CRAN submission. DO NOT EXPORT!

Usage

release_questions()

scatterPlot module server logic

Description

scatterPlot module server logic

Usage

scatterPlot(
  input,
  output,
  session,
  clarion,
  marker.output = NULL,
  plot.method = "static",
  width = "auto",
  height = "auto",
  ppi = 72,
  scale = 1
)

Arguments

input

Shiny's input object

output

Shiny's output object

session

Shiny's session object

clarion

A clarion object. See Clarion. (Supports reactive)

marker.output

Marker module output. See marker.

plot.method

Choose to rather render a 'interactive' or 'static' plot. Defaults to 'static'.

width

Width of the plot in cm. Defaults to minimal size for readable labels and supports reactive.

height

Height of the plot in cm. Defaults to minimal size for readable labels and supports reactive.

ppi

Pixel per inch. Defaults to 72 and supports reactive.

scale

Scale plot size. Defaults to 1, supports reactive.

Details

As markerOutput provides a second dataset used for highlighting it is crucial for it to have the same columnnames as the dataset provided by clarion.

Intersections between marker and clarion will be removed from clarion in favor of highlighting them.

Value

Returns reactive containing data used for plot.

scatterPlot module guide

Description

scatterPlot module guide

Usage

scatterPlotGuide(session, marker = FALSE)

Arguments

session

The shiny session

marker

Logical if marker step should be enabled (Default = FALSE).

Value

A shiny reactive that contains the texts for the Guide steps.

scatterPlot module UI representation

Description

scatterPlot module UI representation

Usage

scatterPlotUI(id)

Arguments

id

The ID of the modules namespace.

Value

A list with HTML tags from tag.

Function to search data for selection

Description

Function to search data for selection

Usage

searchData(
  input,
  choices,
  options = c("=", "<", ">"),
  min. = min(choices, na.rm = TRUE),
  max. = max(choices, na.rm = TRUE)
)

Arguments

input

Vector length one (single) or two (ranged) containing numeric values for selection.

choices

Vector on which input values are applied.

options

Vector on how the input and choices should be compared. It can contain: single = c("=", "<", ">") or ranged = c("inner", "outer").

min.

Minimum value that can be selected on slider (defaults to min(choices)).

max.

Maximum value that can be selected on slider (defaults to max(choices)).

Value

Returns a logical vector with the length of choices, where every matched position is TRUE.

Function to generate sequential (one-sided) color palettes (e.g. for expression, enrichment)

Description

Function to generate sequential (one-sided) color palettes (e.g. for expression, enrichment)

Usage

sequentialPalettes(n)

Arguments

n

Number of colors to generate

Value

A data.table with (named) color palettes of length n

set a log4r logger used within the package

Description

set a log4r logger used within the package

Usage

set_logger(logger, token = NULL)

Arguments

logger

A logger object see create.logger. NULL to disable logging.

token

Set a unique identifier for this logger.

Details

This function will save each logger in the wilson.globals environment. Each logger is stored by the name 'logger'[token] (e.g. 'logger6b821824b0b53b1a3e8f531a34d0d6e6').

Use onSessionEnded to clean up after logging. See onFlush.

TOBIAS TFBS table to clarion parser

Description

Click here for more information about TOBIAS.

Usage

tobias_parser(
  input,
  output,
  filter_columns = NULL,
  filter_pattern = NULL,
  config = system.file("extdata", "tobias_config.json", package = "wilson"),
  omit_NA = FALSE,
  condition_names = NULL,
  condition_pattern = "_bound$",
  in_field_delimiter = ",",
  dec = ".",
  ...
)

Arguments

input

Path to input table

output

Output path.

filter_columns

Either a vector of columnnames or a file containing one columnname per row.

filter_pattern

Keep columns matching the given pattern. Uses parameter filter_columns for matching if set. In the case of no matches a warning will be issued and all columns will be used.

config

Json file containing metadata information for all columns. Will use first occurence for duplicate column names.

omit_NA

Logical whether all rows containing NA should be removed.

condition_names

Vector of condition names. Default = NULL. Used to classify columns not provided in config.

condition_pattern

Used to identify condition names by matching and removing given pattern with grep. Ignored when condition_names is set.

in_field_delimiter

Delimiter for multi value fields. Default = ','.

dec

Decimal separator. Used in file reading and writing.

...

Used as header information.

Details

During conversion the parser will try to use the given config (if provided) to create the Clarion metadata. In the case of insufficient config information it will try to approximate by referencing condition names issuing warnings in the process.

As the format requires an unique id the parser will create one if necessary.

Factor grouping (metadata factor columns) is currently not implemented!

transformation module server logic

Description

The module provides several transformations on a numeric data matrix for the user.

Usage

transformation(
  input,
  output,
  session,
  data,
  transpose = FALSE,
  pseudocount = 1,
  replaceInf = TRUE,
  replaceNA = TRUE
)

Arguments

input

Shiny's input object.

output

Shiny's output object.

session

Shiny's session object.

data

Numeric matrix on which transformation is performed (column-wise). (Supports reactive)

transpose

Whether the matrix should be transposed to enable row-wise transformation. (Supports reactive)

pseudocount

Numeric Variable to add a pseudocount to log-based transformations. (Supports reactive)

replaceInf

Change Infinite to NA, applied after transformation. (Supports reactive)

replaceNA

Change NA to 0, applied after transformation. (Supports reactive)

Value

Namedlist of two containing data and name of the used method. data: Reactive containing the transformed matrix. Infinite values are replaced by NA and NA values are replaced by 0. method: Reactive containing String. transpose: Reactive containing String.

transformation module UI representation

Description

This function provides an input to select a transformation method.

Usage

transformationUI(
  id,
  label = "Transformation",
  selected = "raw",
  choices = list(None = "raw", log2 = "log2", `-log2` = "-log2", log10 = "log10",
    `-log10` = "-log10", `Z score` = "zscore", `regularized log` = "rlog"),
  transposeOptions = FALSE
)

Arguments

id

The ID of the modules namespace.

label

A character vector of length one with the label for the selectInput.

selected

The initially selected value. See selectInput.

choices

Named list of available transformations. Possible transformations are list('None' = "raw", 'log2' = "log2", '-log2' = "-log2", 'log10' = "log10", '-log10' = "-log10", 'Z score' = "zscore", 'regularized log' = "rlog") which is also the default.

transposeOptions

Boolean value if transpose radioButtons are shown (Default = FALSE).

Value

A list with HTML tags from tag.