Help for package RJSplot

Type:

Package

Version:

2.7

Date:

2021-11-30

Title:

Interactive Graphs with R

Description:

Creates interactive graphs with 'R'. It joins the data analysis power of R and the visualization libraries of JavaScript in one package.

URL:

https://rjsplot.usal.es

License:

CC BY-NC-SA 4.0

Depends:

R (≥ 3.0.0)

Suggests:

IRdisplay

NeedsCompilation:

Author:

Carlos Prieto <cprietos@usal.es>, David Barrios <metal@usal.es>

Maintainer:

Carlos Prieto <cprietos@usal.es>

Packaged:

2021-11-30 15:31:42 UTC; dbarrios

Repository:

CRAN

Date/Publication:

2021-12-01 08:40:02 UTC

Interactive graphs with R

Description

Create interactive graphs with 'R'.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Length of human chromosomes based on GRCh37 assembly

Description

Length of human chromosomes based on GRCh37 assembly.

Source

See https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13/.

Cytoband information based on GRCh37

Description

A Data Frame containing cytobands of GRCh37 assembly.

Source

See http://grch37.ensembl.org/Homo_sapiens/Location/Genome.

Length of human chromosomes based on GRCh38 assembly

Description

Length of human chromosomes based on GRCh38 assembly.

Source

See https://www.ncbi.nlm.nih.gov/assembly/883148/.

Cytoband information based on GRCh38

Description

A Data Frame containing cytobands of GRCh38 assembly.

Source

See http://www.ensembl.org/Homo_sapiens/Location/Genome.

Length of human chromosomes based on NCBI36 assembly

Description

Length of human chromosomes based on NCBI36 assembly.

Source

See https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.12/.

Generate a PHP website which runs an R function.

Description

R4web generate a PHP website which runs an R function.

Usage

R4web(...,fnfile,dir)

Arguments

...

one or more newInput objects which will be included as form fields. Form values will be used as parameters for the R script.

fnfile

a character string representing the R script file to be executed with the website.

dir

a "character" string representing the directory where the PHP code will be saved.

Value

The function creates a folder in the working directory of your computer with some PHP files. Resulting folder should be added to the Apache applications directory and enable writting permissions.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Produce interactive bar plot(s).

Description

barplot_rjs produce interactive bar plot(s) of the given values.

Usage

barplot_rjs(height, xlab = "", ylab = "", ylim = NULL, cex = 1,
            plot = TRUE, jupyter = FALSE, dir = tempdir())

Arguments

height

either a vector or matrix of values describing the bars which make up the plot.

xlab

a title for the x axis.

ylab

a title for the y axis.

ylim

a vector with two values which specifies the Y minimun and maximun values in the representation.

cex

number indicating the amount by which plotting text and symbols should be scaled relative to the default.

plot

open resulting graph in your browser.

jupyter

embed the graph as an iframe into a Jupyter Notebook.

dir

a "character" string representing the directory where the graph will be saved.

Value

The function creates a folder in your computer with an HTML document named index.html which contains the graph. This file can be directly opened with your browser.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Examples

## Create an interactive barplot in a temporal directory of your local machine
## Live examples on https://rjsplot.usal.es
if(interactive()){
barplot_rjs(USArrests, "states", "arrests")
}

Produce interactive box-and-whisker plot(s).

Description

boxplot_rjs produce interactive box-and-whisker plot(s) of the given values.

Usage

boxplot_rjs(data, xlab = "", ylab = "",
            outline = TRUE, col = NULL, ylim = NULL, cex = 1,
            plot = TRUE, jupyter = FALSE, dir = tempdir())

Arguments

data

a Data Frame or Matrix from which the data for each box will be taken.

outline

if outline is not true, the outliers are not drawn.

col

if 'col' is non-null it is assumed to contain colors to be used to colour the bodies of the box plots.

xlab

a title for the x axis.

ylab

a title for the y axis.

ylim

a vector with two values which specifies the Y minimun and maximun values in the representation.

cex

number indicating the amount by which plotting text and symbols should be scaled relative to the default.

plot

open resulting graph in your browser.

jupyter

embed the graph as an iframe into a Jupyter Notebook.

dir

a "character" string representing the directory where the graph will be saved.

Value

The function creates a folder in your computer with an HTML document named index.html which contains the graph. This file can be directly opened with your browser.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Examples

## Create an interactive boxplot in a temporal directory of your local machine
## Live examples on https://rjsplot.usal.es
if(interactive()){
boxplot_rjs(attitude, "attitude", "favourable responses")
}

Produce interactive bubble plots.

Description

bubbles_rjs produce interactive bubble plot(s) of the given values.

Usage

bubbles_rjs(data, size = NULL, plot = TRUE, jupyter = FALSE, dir = tempdir())

Arguments

data

a numeric Data Frame or Matrix with two columns and one row per bubble which contains represented values for each bubble. Row names will be used as bubble names.

size

a vector giving each bubble size.

plot

open resulting graph in your browser.

jupyter

embed the graph as an iframe into a Jupyter Notebook.

dir

a "character" string representing the directory where the graph will be saved.

Value

The function creates a folder in your computer with an HTML document named index.html which contains the graph. This file can be directly opened with your browser.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Examples

## Create an interactive barplot in a temporal directory of your local machine
## Live examples on https://rjsplot.usal.es
if(interactive()){
bubbles_rjs(scale(mtcars[,c("mpg","hp")],FALSE),mtcars$wt)
}

Pruduce a circular sequence viewer.

Description

circularfv_rjs creates a circular sequence viewer.

Usage

circularfv_rjs(sequence, features = FALSE,
               plot = TRUE, jupyter = FALSE, dir = tempdir())

Arguments

sequence

a "character" string giving the DNA sequence.

features

Data Frame with the segments that will be seen in the viewer. It cotains 5 columns which describes the identifier, start coordinate, stop coordinate, segment type and segment color.

plot

open resulting graph in your browser.

jupyter

embed the graph as an iframe into a Jupyter Notebook.

dir

a "character" string representing the directory where the graph will be saved.

Value

The function creates a folder in your computer with an HTML document named index.html which contains the graph. This file can be directly opened with your browser.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Examples

if(interactive()){
## Creates a circular sequence viewer in a temporal directory of your local machine
## Generate test input data
sequence <- paste(sample(c("c","a","t","g"), 10000, replace = TRUE), collapse = "")
data <- matrix(round(runif(12,0,10000)),6,2)
features <- data.frame(id = 0:5, start = data[,1], stop = data[,2],
type = c("voluptate","non","voluptate","sit","et","proident"),
color = c("SandyBrown","Tan","Wheat","SteelBlue","LightSkyBlue","LightBlue"))

## Create the circular sequence viewver
circularfv_rjs(sequence, features)
}

Creates a genome assembly for `genomemap_rjs` or `manhattan_rjs`.

Description

createAssembly create assemblies for their use as parameter of genomemap_rjs or manhattan_rjs.

Usage

createAssembly(name, size)

Arguments

name

a vector with the chomosome or scaffold names.

size

a vector with the chomosome or scaffold sizes.

Value

a data frame in BED format to be used as an assembly in genomemap_rjs or manhattan_rjs.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Examples

## Creates a fake genome assembly for its posterior use as parameter of genomemap or manhattan plot
## Live examples and full tutorial on https://rjsplot.usal.es

## Generate a test assembly with three scaffolds
assembly <- createAssembly(c("scaffold1","scaffold2","scaffold3"), c(1000000,800000,650000))

Draw a Dendrogram.

Description

dendrogram_rjs creates a dendrogram.

Usage

dendrogram_rjs(data, metadata = NULL, method = "complete", cex = 1,
               plot = TRUE, jupyter = FALSE, dir = tempdir())

Arguments

data

a dissimilarity object of class dist (p.e. produced by function dist).

metadata

a data frame with metadata information for leaf features (p.e. sample phenotypes). Corresponding Leaf/Sample should be provided as row name.

method

Name of the agglomeration method to be used. It should be (an unambiguous abbreviation of) one of "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC).

cex

number indicating the amount by which plotting text and symbols should be scaled relative to the default.

plot

open resulting graph in your browser.

jupyter

embed the graph as an iframe into a Jupyter Notebook.

dir

A "character" string representing the directory where the graph will be saved.

Value

The function creates a folder in your computer with an HTML document named index.html which contains the graph. This file can be directly opened with your browser.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Examples

## Create a dendrogram in a temporal directory of your local machine
## Live examples on https://rjsplot.usal.es
if(interactive()){
dendrogram_rjs(dist(USArrests),USArrests)
}

Draw an interactive density plot.

Description

densityplot_rjs creates density plots.

Usage

densityplot_rjs(data, xlab = "", ylab = "", cex = 1,
                plot = TRUE, jupyter = FALSE, dir = tempdir())

Arguments

data

a data frame from which distribution will be represented for each column.

xlab

a title for the x axis.

ylab

a title for the y axis.

cex

number indicating the amount by which plotting text and symbols should be scaled relative to the default.

plot

open resulting graph in your browser.

jupyter

embed the graph as an iframe into a Jupyter Notebook.

dir

a "character" string representing the directory where the graph will be saved.

Value

The function creates a folder in your computer with an HTML document named index.html which contains the graph. This file can be directly opened with your browser.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Examples

## Creates a density plot in a temporal directory of your local machine
## Live examples on https://rjsplot.usal.es

if(interactive()){
## Generate test input data
data <- data.frame(Uni05 = (1:100)/21, Norm = rnorm(100), `5T` = rt(100, df = 5),
Gam2 = rgamma(100, shape = 2))

# Create the density plot
densityplot_rjs(data, "x", "y")
}

Create an interative genome map.

Description

genomemap_rjs creates an interactive genome map.

Usage

genomemap_rjs(assembly, track = NULL, plot = TRUE, jupyter = FALSE, dir = tempdir())

Arguments

assembly

a genome assembly data frame. RJSplot provides human assemblies (NCBI36, GRCh37, GRCh38), human assemblies with cytobands (GRCh37.bands or GRCh38.bands), or methods for creating your own assembly from a FASTA file getAssemblyFromFasta.

track

a data frame with values to represent on the genome map (chromosome, position, value).

plot

open resulting graph in your browser.

jupyter

embed the graph as an iframe into a Jupyter Notebook.

dir

a "character" string representing the directory where the graph will be saved.

Value

The function creates a folder in your computer with an HTML document named index.html which contains the graph. This file can be directly opened with Firefox. If you want to open this file stored in your local machine with other Web browser, please visit the help section on the RJSplot Web site (https://rjsplot.usal.es).

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Examples

## Create an interactive Genome map in a temporal directory of your local machine
## Live examples on https://rjsplot.usal.es

if(interactive()){
# Create test data
chr <- character()
pos <- numeric()

for(i in 1:nrow(GRCh38)){
  chr <- c(chr,as.character(rep(GRCh38[i,"chr"],100)))
  pos <- c(pos,sample(GRCh38[i,"start"]:GRCh38[i,"end"],100))
}

value <- round(rexp(length(pos)),2)

# Create a genome map
track <- data.frame(chr,pos,pos+1,NA,value)
genomemap_rjs(GRCh38.bands, track)
}

Create an assembly from a FASTA file for its use as parameter of `genomemap_rjs` or `manhattan_rjs`.

Description

getAssemblyFromFasta create assemblies from a FASTA file for their use as parameter of genomemap_rjs or manhattan_rjs.

Usage

getAssemblyFromFasta(fasta)

Arguments

fasta

a "character" string representing the input Fasta file to be added in the genome browser.

Value

a data frame in BED format ready to use as an assembly in genomemap_rjs or manhattan_rjs.

Note

FASTA format is a text-based format for representing either nucleotide sequences or peptide sequences, in which nucleotides or amino acids are represented using single-letter codes.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Examples

## Live examples and full tutorial on https://rjsplot.usal.es

Produce an interactive heatmap.

Description

heatmap_rjs creates interactive heatmaps.

Usage

heatmap_rjs(data, metadata = NULL, scale = c("row", "column", "none"),
  cluster = TRUE, color = c("Reds", "Greens", "Blues", "RdBkGr", "RdWhBu"),
  na.color = "transparent", cex = 1, plot = TRUE, jupyter = FALSE, 
  dir = tempdir(), distfun = dist, hclustfun = hclust)

Arguments

data

numeric matrix of the values to be plotted.

metadata

a data frame with metadata information for column features (p.e. sample phenotypes). Samples are given in rows and features in columns.

scale

character indicating if the values should be centered and scaled in either the row direction or the column direction, or none. The default value is "none".

cluster

logical value to enable (TRUE) or disable (FALSE) data clustering.

color

character indicating the color scale to paint values. The default value is "Blues".

na.color

character indicating the color to use for missing values. Transparent by default.

cex

number indicating the amount by which plotting text and symbols should be scaled relative to the default.

plot

open resulting graph in your browser.

jupyter

embed the graph as an iframe into a Jupyter Notebook.

dir

a "character" string representing the directory where the graph will be saved.

distfun

function used to compute the distance between rows and columns.

hclustfun

function used to compute the hierarchical clustering.

Value

The function creates a folder in your computer with an HTML document named index.html which contains the graph. This file can be directly opened with your browser.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Examples

## Create an interactive heatmap in a temporal directory of your local machine
## Live examples on https://rjsplot.usal.es
if(interactive()){
metadata <- data.frame(phenotype1 = sample(c("yes","no"),ncol(mtcars),TRUE),
                       phenotype2 = sample(1:5,ncol(mtcars),TRUE))

heatmap_rjs(data.matrix(mtcars), metadata, scale="column")
}

Produce interactive hive plot

Description

hiveplot_rjs creates an interactive hive plot.

Usage

hiveplot_rjs(links, nodes = NULL, group = NULL, size = NULL, color = NULL,
             cex = 1, plot = TRUE, jupyter = FALSE, dir = tempdir())

Arguments

links

an edge list table stored in a data frame with three possible columns (source node id, target node id and link value).

nodes

node attributes stored in a data frame with rownames as node id.

group

column name of nodes data frame which describes visualized axes.

size

column name of nodes data frame which describes each node size.

color

column name of nodes data frame which describes each node color.

cex

number indicating the amount by which plotting text and symbols should be scaled relative to the default.

plot

open resulting graph in your browser.

jupyter

embed the graph as an iframe into a Jupyter Notebook.

dir

a "character" string representing the directory where the graph will be saved.

Value

The function creates a folder in your computer with an HTML document named index.html which contains the graph. This file can be directly opened with your browser.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Examples

## Create an interactive hive plot in a temporal directory of your local machine
## Live examples on https://rjsplot.usal.es

if(interactive()){
# Prepare data
x <- 1-cor(t(mtcars))

source <- rep(rownames(x),nrow(x))
target <- rep(rownames(x),rep(ncol(x),nrow(x)))
links <- data.frame(source=source,target=target,value=as.vector(x))

# Generate the hive plot
hiveplot_rjs(links, mtcars, group = "cyl", size = "wt", color = "carb")
}

Create an interactive manhattan plot

Description

manhattan_rjs creates an interactive Manhattan plot.

Usage

manhattan_rjs(data, assembly, axisv, distv, cell = 1e+06,
  outliers = TRUE, ylab = "score", yscale = NULL,
  cex = 1, plot = TRUE, jupyter = FALSE, dir = tempdir())

Arguments

data

a data frame with four columns (identifier, chromosome/scaffold, position, score).

assembly

a data frame with an assembly to be used. It should be one of the following human assemblies data frames provided by RJSplot: NCBI36, GRCh37, GRCh38.

axisv

value for the coordinate of the main horizontal axis.

distv

distance between the main horizontal axis and the secondary axes (which stablishes the limit for the outlier representation).

cell

segment size which is represented.

outliers

logical value to enable (TRUE) or disable (FALSE) outliers.

ylab

a title for the y axis.

yscale

a vector with two values which specifies the minimun and maximun limits in the representation. By default maximun and minimun scores are taken as the limits.

cex

number indicating the amount by which plotting text and symbols should be scaled relative to the default.

plot

open resulting graph in your browser.

jupyter

embed the graph as an iframe into a Jupyter Notebook.

dir

a "character" string representing the directory where the graph will be saved.

Value

The function creates a folder in your computer with an HTML document named index.html which contains the graph. This file can be directly opened with your browser.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Examples


## Create an interactive Manhattan plot in a temporal directory of your local machine
## Live examples on https://rjsplot.usal.es

if(interactive()){
# Create test data
chr <- character()
pos <- numeric()

for(i in 1:nrow(GRCh38)){
  chr <- c(chr,as.character(rep(GRCh38[i,"chr"],100)))
  pos <- c(pos,sample(GRCh38[i,"start"]:GRCh38[i,"end"],100))
}

value <- round(rexp(length(pos)),2)

# Create a manhattan plot
data <- data.frame(paste0("ProbeSet_",seq_along(pos)),chr,pos,value)
manhattan_rjs(data, GRCh38, 0, 1, 0, TRUE, "log2Ratio")
}

Produce interactive network graph

Description

network_rjs creates an interactive network graph.

Usage

network_rjs(links, nodes = NULL,
            weight = NULL, linkLabel = NULL, linkColor = NULL,
            group = NULL, size = NULL, color = NULL, label = NULL,
            nodeColorScale = c("RdBk","RdBkGr"), cex = 1, 
            plot = TRUE, jupyter = FALSE, dir = tempdir())

Arguments

links

an edge list table stored in a data frame with at least two columns (source node id and target node id).

nodes

a node list stored in a data frame object with rownames as node id.

weight

a vector giving the column of links to show as weight. If NULL but third links column is numeric, this one will be used as weight.

linkLabel

a vector giving the column of links to show as link text.

linkColor

a vector giving the column of links to compute link color or directly a vector of colors.

group

a vector giving the column of nodes to show as group.

size

a vector giving the column of nodes to show as size.

color

a vector giving the column of nodes to compute node color or directly a vector of colors.

label

a vector giving the column of nodes to show as label.

nodeColorScale

a "character" string representing the color scale applied to nodes by default.

cex

number indicating the amount by which plotting text and symbols should be scaled relative to the default.

plot

open resulting graph in your browser.

jupyter

embed the graph as an iframe into a Jupyter Notebook.

dir

a "character" string representing the directory where the graph will be saved.

Value

The function creates a folder in your computer with an HTML document named index.html which contains the graph. This file can be directly opened with your browser.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Examples

## Create an interactive network graph in a temporal directory of your local machine
## Live examples on https://rjsplot.usal.es

if(interactive()){
# Prepare data
x <- 1-cor(t(mtcars))

source <- rep(rownames(x),nrow(x))
target <- rep(rownames(x),rep(ncol(x),nrow(x)))
links <- data.frame(source=source,target=target,value=as.vector(x))

# Generate the network graph
network_rjs(links[links[,3]>0.1,], mtcars, group = "cyl", size = "hp", color = "mpg")
}

Produce a `newInput` object for `R4web`.

Description

newInput produce newInput object for R4web.

Usage

newInput(name, type = c("character","numeric","matrix","data.frame","factor"),
         default = "", levels = NULL, multi = FALSE)

Arguments

name

character string with the variable name.

type

character string which describes the variable type. Possible values are "character", "numeric", "matrix", "data.frame" or "factor".

default

default value for this input.

levels

a vector with the possible input values. It is described only for factor data type.

multi

boolean value which indicates if multiple selection are enabled for this input. It is described only for factor data type.

Value

Return a newInput object.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Produce interactive pie charts.

Description

piechart_rjs produce interactive pie charts.

Usage

piechart_rjs(data, cex = 1, plot = TRUE, jupyter = FALSE, dir = tempdir())

Arguments

data

a Data Frame or Matrix from which the data for each pie will be taken.

cex

number indicating the amount by which plotting text and symbols should be scaled relative to the default.

plot

open resulting graph in your browser.

jupyter

embed the graph as an iframe into a Jupyter Notebook.

dir

a "character" string representing the directory where the graph will be saved.

Value

The function creates a folder in your computer with an HTML document named index.html which contains the graph. This file can be directly opened with your browser.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Examples

## Create an interactive pie chart in a temporal directory of your local machine
## Live examples on https://rjsplot.usal.es
if(interactive()){
piechart_rjs(VADeaths)
}

Create a report web page.

Description

report_rjs creates a report web page.

Usage

report_rjs(dir = "RJSreport")
addCSS2report(report,css)
addHTML2report(report,HTML)
addParagraph2report(report,p)
addPlot2report(report,plot,height=600)
addImage2report(report,img)

Arguments

dir

a "character" string representing the directory where the report will be saved.

report

a RJSreport object produced by the function report_rjs.

css

a character string representing the CSS path to be added.

HTML

a character string giving the HTML code to be added.

p

a character string giving the new paragraph to be added.

plot

a character string representing the plot directory to be added.

height

an integer vector giving a default height of the plot.

img

a character string representing the image path to be added.

Value

The function creates a folder in your computer with an HTML document named index.html which contains the report. This file can be directly opened with your browser.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Produce and interactive 3D Scatter plot (XYZ plot).

Description

scatter3d_rjs generates an interactive 3D Scatter Plot.

Usage

scatter3d_rjs(x, y, z, color="#000", xlab = "x", ylab = "y", zlab = "z",
              plot = TRUE, jupyter = FALSE, dir = tempdir())

Arguments

x

a vector with the x data of each point.

y

a vector with the y data of each point.

z

a vector with the z data of each point.

xlab

a title for the x axis.

ylab

a title for the y axis.

zlab

a title for the z axis.

color

a vector with the colour of each represented point.

plot

open resulting graph in your browser.

jupyter

embed the graph as an iframe into a Jupyter Notebook.

dir

a "character" string representing the directory where the graph will be saved.

Value

The function creates a folder in your computer with an HTML document named index.html which contains the graph. This file can be directly opened with your browser.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Examples

## Create an interactive 3D Scatter plot in a temporal directory of your local machine
## Live examples on https://rjsplot.usal.es

# 3D Scatter plot creation
if(interactive()){
scatter3d_rjs(iris$Sepal.Width, iris$Sepal.Length, iris$Petal.Width,
  color = iris$Species, xlab = "Sepal Width (cm)", ylab = "Sepal Length (cm)",
  zlab = "Petal Width (cm)")
}

Produce and interactive Scatter plot (XY plot).

Description

scatterplot_rjs generates an interactive Scatter Plot.

Usage

scatterplot_rjs(x, y, id = NULL, xlab = "", ylab = "",
                xlim = NULL, ylim = NULL, col = NULL,
                pch = NULL, abline.x = NULL, abline.y = NULL, cex = 1,
                plot = TRUE, jupyter = FALSE, dir = tempdir())

Arguments

x

a vector with the x data of each point.

y

a vector with the y data of each point.

id

a vector giving the id of each point.

xlab

a title for the x axis.

ylab

a title for the y axis.

xlim

a vector with two values which specifies the X minimun and maximun values in the representation.

ylim

a vector with two values which specifies the Y minimun and maximun values in the representation.

col

a vector with the colour of each represented point.

pch

a character vector with the shape of each point. It should be one of: 1-"circle", 2-"triangle-up", 3-"cross", 4-"square", 5-"diamond", 6-"triangle-down".

abline.x

a numeric vector with x coordenates where a vertical line will be placed.

abline.y

a numeric vector with y coordenates where a horizontal line will be placed.

cex

number indicating the amount by which plotting text and symbols should be scaled relative to the default.

plot

open resulting graph in your browser.

jupyter

embed the graph as an iframe into a Jupyter Notebook.

dir

a "character" string representing the directory where the graph will be saved.

Value

The function creates a folder in your computer with an HTML document named index.html which contains the graph. This file can be directly opened with your browser.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Examples

## Create an interactive Scatter plot in a temporal directory of your local machine
## Live examples on https://rjsplot.usal.es

if(interactive()){
# Scatter plot creation
scatterplot_rjs(iris$Sepal.Width, iris$Sepal.Length,
  abline.x = c(3.4,3.8), abline.y = c(5.8,7),
  col = iris$Species, pch = as.numeric(iris$Species), id = iris$Species,
  xlab = "Sepal Width (cm)", ylab = "Sepal Length (cm)")
}

Produce and interactive 3D surface.

Description

surface3d_rjs generates an interactive 3D surface.

Usage

surface3d_rjs(x, color = "#fff", xlab = "x", ylab = "y", zlab = "z",
              plot = TRUE, jupyter = FALSE, dir = tempdir())

Arguments

x

numeric matrix of the values to be plotted.

color

a vector with colors to construct the color scale.

xlab

a title for the x axis.

ylab

a title for the y axis.

zlab

a title for the z axis.

plot

open resulting graph in your browser.

jupyter

embed the graph as an iframe into a Jupyter Notebook.

dir

a "character" string representing the directory where the graph will be saved.

Value

The function creates a folder in your computer with an HTML document named index.html which contains the graph. This file can be directly opened with your browser.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Examples

## Create an interactive 3D Surface in a temporal directory of your local machine
## Live examples on https://rjsplot.usal.es

if(interactive()){
# 3D surface creation
surface3d_rjs(volcano,color=c("red","green"))
}

Creates a Symetric Heatmap representation.

Description

symheatmap_rjs creates an interactive symetric heatmap.

Usage

symheatmap_rjs(links, nodes = NULL, group = NULL, label = NULL, cex = 1,
               plot = TRUE, jupyter = FALSE, dir = tempdir())

Arguments

links

an edge list table stored in a data frame with three possible columns (source node id, target node id and a link value).

nodes

a node list stored in a data frame object with rownames as node id.

group

a vector giving the column of nodes to show as group.

label

a vector giving the column of nodes to show as label.

cex

number indicating the amount by which plotting text and symbols should be scaled relative to the default.

plot

open resulting graph in your browser.

jupyter

embed the graph as an iframe into a Jupyter Notebook.

dir

a "character" string representing the directory where the graph will be saved.

Value

The function creates a folder in your computer with an HTML document named index.html which contains the graph. This file can be directly opened with your browser.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Examples

## Create an interactive symetric heatmap in a temporal directory of your local machine
## Live examples on https://rjsplot.usal.es

if(interactive()){
# prepare data
x <- 1-cor(t(mtcars))

source <- rep(rownames(x),nrow(x))
target <- rep(rownames(x),rep(ncol(x),nrow(x)))
links <- data.frame(source=source,target=target,value=as.vector(x))

# Create symetric heatmap
symheatmap_rjs(links, mtcars, group = "cyl")
}

Produce interactive html tables.

Description

tables_rjs produce interactive html tables of the given values.

Usage

tables_rjs(data, plot = TRUE, jupyter = FALSE, dir = tempdir())

Arguments

data

a Data Frame or Matrix to display.

plot

open resulting table in your browser.

jupyter

embed the graph as an iframe into a Jupyter Notebook.

dir

a "character" string representing the directory where the graph will be saved.

Value

The function creates a folder in your computer with an HTML document named index.html which contains the table. This file can be directly opened with your browser.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Examples

## Create an interactive html table in a temporal directory of your local machine
## Live examples on https://rjsplot.usal.es
if(interactive()){
tables_rjs(swiss)
}

Draw a wordcloud.

Description

wordcloud_rjs creates a wordcloud.

Usage

wordcloud_rjs(data, plot = TRUE, jupyter = FALSE, dir = tempdir())

Arguments

data

a two column data Frame with the words to display and their frequency.

plot

open resulting graph in your browser.

jupyter

embed the graph as an iframe into a Jupyter Notebook.

dir

a "character" string representing the directory where the graph will be saved.

Value

The function creates a folder in your computer with an HTML document named index.html which contains the graph. This file can be directly opened with your browser.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

Examples

## Create an interactive heatmap in a temporal directory of your local machine
## Live examples on https://rjsplot.usal.es

## Format test data
words <- data.frame(word = rownames(USArrests), freq = USArrests[,4])

# Create WordCloud
if(interactive()){
wordcloud_rjs(words)
}

Interactive graphs with R

Description

Author(s)

See Also

Length of human chromosomes based on GRCh37 assembly

Description

Source

Cytoband information based on GRCh37

Description

Source

Length of human chromosomes based on GRCh38 assembly

Description

Source

Cytoband information based on GRCh38

Description

Source

Length of human chromosomes based on NCBI36 assembly

Description

Source

Generate a PHP website which runs an R function.

Description

Usage

Arguments

Value

Author(s)

See Also

Produce interactive bar plot(s).

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Produce interactive box-and-whisker plot(s).

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Produce interactive bubble plots.

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Pruduce a circular sequence viewer.

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Creates a genome assembly for genomemap_rjs or manhattan_rjs.

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Draw a Dendrogram.

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Draw an interactive density plot.

Description

Usage

Arguments

Value

Author(s)

Creates a genome assembly for `genomemap_rjs` or `manhattan_rjs`.

Create an assembly from a FASTA file for its use as parameter of `genomemap_rjs` or `manhattan_rjs`.

Produce a `newInput` object for `R4web`.