Package {nVennR2}

nVennR2: An Interface to 'nVenn2'

Description

Creates quasi-proportional Venn diagrams with an arbitrary number of sets. It is related to the old 'nVennR' package, but the algorithm and use have been reworked.

Author(s)

Maintainer: Victor Quesada quesadavictor@uniovi.es [copyright holder]

See Also

Useful links:

• https://github.com/vqf/nVennR2

• Report bugs at https://github.com/vqf/nVennR2/issues

Estimates the time taken by minimization steps when preparing a diagram with the exhaustive method at a given depth

Description

Estimates the time taken by minimization steps when preparing a diagram with the exhaustive method at a given depth

Usage

estimateExhaustiveRunTime(desc, maxlevel = 0L, byCol = 0L)

Arguments

Value

float Estimated time for steps 3 and 4 in seconds. In case of error, the returned value is -1.

Examples

estimateExhaustiveRunTime(exampledf, 4)

Example data frame.

Description

A dataset containing programming preferences from 18 employees. This data set was provided by user Krantz to inquire about nVennR2

Usage

exampledf

Format

A data frame with 18 rows and 3 variables:

Employee

Employee ID

SAS

Employee uses SAS

Python

Employee uses Python

R

Employee uses R

Source

https://stackoverflow.com/questions/49471565/transforming-data-to-create-generalized-quasi-proportional-venn-diagrams-using

Gets a list of the elements in a region of the diagram

Description

Gets a list of the elements in a region of the diagram

Usage

getVennRegion(nVennObj, n)

Arguments

Details

An integer expresses a region by considering its binary representation in reverse. A 1 in a position means "belongs to" and a 0 or empty position means "does not belong to". Thus, the binary representation of 19 (10011), read from right to left, means "region that belongs to sets 1, 2 and 5 and does not belong to any other set".

A vector of set names expresses a region by giving the sets the region belongs to. It is understood that the region does not belong to any other set.

Value

List of set names.

Examples

myv <- nVennDiagram(list(Set1=c("a", "b", "c"), Set2=c("a", "c", "d")), verbose=FALSE)
#Both commands are equivalent:
getVennRegion(myv, 3)
getVennRegion(myv, c("Set1", "Set2"))

Gets the names of the sets

Description

Gets the names of the sets

Usage

getVennSetNames(nVennObj)

Arguments

Value

List of set names.

Examples

myv <- nVennDiagram(list(Set1=c("a", "b", "c"), Set2=c("a", "c", "d")), verbose=FALSE)
getVennSetNames(myv)

Get the svg code of an nVenn diagram

Description

Get the svg code of an nVenn diagram

Usage

getVennSvg(nVennObj)

Arguments

Details

The code returned by the funciton can be saved to a file and then edited with vectorial image software. This can be done directly with nVennDiagram() or plotVenn() by using the outFile param.

Value

String with svg code.

Examples

myv <- nVennDiagram(list(Set1=c("a", "b", "c"), Set2=c("a", "c", "d")), verbose=FALSE)
getVennSvg(myv)

Lists the elements in every region of the diagram

Description

Lists the elements in every region of the diagram

Usage

listVennRegions(nVennObj, showEmpty = FALSE)

Arguments

Value

List of non-empty regions with the elements contained

Examples

myv <- nVennDiagram(list(Set1=c("a", "b", "c"), Set2=c("a", "c", "d")), verbose=FALSE)
mylist <- listVennRegions(myv)
mylist

Creates nVenn plot

Description

Creates nVenn plot

Usage

nVennDiagram(
  desc,
  plot = TRUE,
  outFile = "",
  systemShow = FALSE,
  verbose = TRUE,
  maxlevel = 0L,
  byCol = 0L
)

Arguments

Details

A list of lists contains inner lists with a name, which will be the corresponding set name. A dataframe can be used in the same way.

The input can also be a text containing a table, possibly with missing values. If a text is provided, the package will try to guess if each set is encoded in columns or rows (use byCol to force) and which character separates fields (usually tab, space or comma). If the text describes a valid text file path, the contents of the file will be used.

Value

nVenn object. As a side effect, shows the nVenn plot. In case of error, returns null object.

Examples

myv <- nVennDiagram(list(Set1=c("a", "b", "c"), Set2=c("a", "c", "d")), verbose=FALSE)

nVennR2

Description

An interface to nVenn2 to create n-dimensional, quasi-proportional Venn diagrams.

Details

The input for nVennR2 is a list of lists or a text table. The dataset exampledf contains an example of a list of lists, where each internal list has a name for the set and some set elements. The result will be a Venn diagram where each region is represented by a circle whose area is approximately proportional to the number of elements in that region. Each circle has two labels. The number in a larger font size represents the number of elements in the region. The smaller numbers in parentheses show which sets the region belongs to.

A diagram is created with nVennDiagram() and plotted and/or saved with plotVenn(). The appearance of the plot can be changed with setVennOpts() and setVennColors(). If a plot is saved, the resulting svg file can be loaded again with readVennSVG().

Value

nVennObj. An nVenn object with the information needed to represent and edit the diagram, and to explore its regions.

Author(s)

Victor Quesada, Universidad de Oviedo (Spain).

Examples

library(nVennR2)
myv <- nVennDiagram(exampledf, verbose=FALSE)
myv <- setVennOpts(myv, opacity=0.2, fontSize=14)

Plot nVenn diagram

Description

The nVenn diagram is generated in the plot window by default. If this is not possible, parameters outFile and systemShow may be used to export the SVG figure.

Usage

plotVenn(nVennObj, outFile = "", systemShow = FALSE)

Arguments

Value

Nothing. If nVennObj is correct and the system supports it, the diagram is plotted in the plot window.

Examples

myv <- nVennDiagram(list(Set1=c("a", "b", "c"), Set2=c("a", "c", "d")), verbose=FALSE)
plotVenn(myv) 

Creates nVenn plot

Description

Creates nVenn plot

Usage

readVennSVG(svgFile, plot = TRUE, outFile = "", systemShow = FALSE)

Arguments

Details

In principle, this function should work with any SVG or HTML file created by nVenn, with either nVennR2, a web interface or nVennPy.

Value

nVenn object.

Examples

if (file.exists('example.svg')){
  readVennSVG('example.svg')
}

Rotate a diagram

Description

Rotate a diagram

Usage

rotateVenn(nVennObj, angle, plot = TRUE)

Arguments

Value

nVenn object.

Examples

myv <- nVennDiagram(list(Set1=c("a", "b", "c"), Set2=c("a", "c", "d")), verbose=FALSE)
myv <- rotateVenn(myv, 45)

Change a set color

Description

Change a set color

Usage

setVennColor(nVennObj, setName, color, plot = TRUE)

Arguments

Value

nVenn object with the change in color for the set.

Examples

myv <- nVennDiagram(list(Set1=c("a", "b", "c"), Set2=c("a", "c", "d")), verbose=FALSE)
myv <- setVennColor(myv, "Set2", "black")
myv <- setVennColor(myv, "Set1", "#ffff00")

Change set colors

Description

Change set colors

Usage

setVennColors(nVennObj, colorList, plot = TRUE)

Arguments

Details

If a vector of svg-formatted colors is provided, they will be used in the same order. This is a good way to create and use a custom color palette. If a list is used, the function will call setVennColor() with the names in the list.

It is important to notice that each color must be a valid color in SVG format. The value is not checked, and therefore an incorrect value may break the plot in plotVenn() or lead to unexpected results.

Value

nVenn object with changed set colors.

Examples

myv <- nVennDiagram(list(Set1=c("a", "b", "c"), Set2=c("a", "c", "d")), verbose=FALSE)
mypalette <- c("black", "#ffff00", "red")
myv <- setVennColors(myv, mypalette)

Set graphical parameters of an nVenn object diagram.

Description

The function returns an object whose parameters will change the way the diagram is plotted.

Usage

setVennOpts(
  nVennObj,
  opacity = 0.4,
  fontSize = 12,
  lineWidth = 1,
  palette = 0,
  showRegions = TRUE,
  showWeights = TRUE,
  plot = TRUE
)

Arguments

Value

nVennObj with graphical options set.

Examples

myv <- nVennDiagram(exampledf)
myv <- setVennOpts(myv, showRegions=FALSE, opacity=0.2, lineWidth=2)

Change the color palette for a diagram

Description

Change the color palette for a diagram

Usage

setVennPalette(nVennObj, palette = 0, plot = TRUE)

Arguments

Details

The color palette for a diagram can also be set with setVennOpts(), but with a small difference. If a set color has been set with setVennColor(), setVennPalette() will override and delete that setting, while setVennOpts() will not. This way, one can have a color defined for a set and change the colors of the rest of sets with setVennOpts() or reset every color to the pre-defined palette with setVennPalette().

Value

nVenn object with the palette set to the requested value.

See Also

setVennOpts() for an alternative way to change the color palette.

Examples

myv <- nVennDiagram(list(Set1=c("a", "b", "c"), Set2=c("a", "c", "d")), verbose=FALSE)
myv <- setVennPalette(myv, 2)
myv <- setVennPalette(myv, 3)

Set nVenn diagram appearance

Description

Set nVenn diagram appearance

Usage

setVennSkin(nVennObj, params, plot = TRUE)

Arguments

Details

Running this function is equivalent to running setVennOpts() repeatedly. The advantage is that setVennSkin() can set multiple parameters at the same time. The same params list can be used on multiple nVenn objects as a theme.

The only valid parameters for params are those in setVennOpts(), palette and colors.

Value

nVenn object with skin applied

Examples

theme <- list(opacity=0.2, lineWidth=2, fontSize=14, showRegions=FALSE,
              palette=2, colors=c("black"))
myv <- nVennDiagram(exampledf)
myv <- setVennSkin(myv, theme)