| 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. |
| Authors: | Carlos Prieto <[email protected]>, David Barrios <[email protected]> |
| Maintainer: | Carlos Prieto <[email protected]> |
| License: | CC BY-NC-SA 4.0 |
| Version: | 2.7 |
| Built: | 2024-10-31 21:13:21 UTC |
| Source: | CRAN |
barplot_rjs produce interactive bar plot(s) of the given values.
barplot_rjs(height, xlab = "", ylab = "", ylim = NULL, cex = 1, plot = TRUE, jupyter = FALSE, dir = tempdir())barplot_rjs(height, xlab = "", ylab = "", ylim = NULL, cex = 1, plot = TRUE, jupyter = FALSE, dir = tempdir())
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. |
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.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.
## 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") }## 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") }
boxplot_rjs produce interactive box-and-whisker plot(s) of the given values.
boxplot_rjs(data, xlab = "", ylab = "", outline = TRUE, col = NULL, ylim = NULL, cex = 1, plot = TRUE, jupyter = FALSE, dir = tempdir())boxplot_rjs(data, xlab = "", ylab = "", outline = TRUE, col = NULL, ylim = NULL, cex = 1, plot = TRUE, jupyter = FALSE, dir = tempdir())
data |
a Data Frame or Matrix from which the data for each box will be taken. |
outline |
if |
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. |
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.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.
## 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") }## 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") }
bubbles_rjs produce interactive bubble plot(s) of the given values.
bubbles_rjs(data, size = NULL, plot = TRUE, jupyter = FALSE, dir = tempdir())bubbles_rjs(data, size = NULL, plot = TRUE, jupyter = FALSE, dir = tempdir())
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. |
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.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.
## 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$wt) }## Create an interactive barplot in a temporal directory of your local machine ## Live examples on https://rjsplot.usal.es if(interactive()){ bubbles_rjs(scale(mtcars[,c("mpg","hp")],FALSE),mtcars$wt) }
circularfv_rjs creates a circular sequence viewer.
circularfv_rjs(sequence, features = FALSE, plot = TRUE, jupyter = FALSE, dir = tempdir())circularfv_rjs(sequence, features = FALSE, plot = TRUE, jupyter = FALSE, dir = tempdir())
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. |
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.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.
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) }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) }
genomemap_rjs or manhattan_rjs.createAssembly create assemblies for their use as parameter of genomemap_rjs or manhattan_rjs.
createAssembly(name, size)createAssembly(name, size)
name |
a vector with the chomosome or scaffold names. |
size |
a vector with the chomosome or scaffold sizes. |
a data frame in BED format to be used as an assembly in genomemap_rjs or manhattan_rjs.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
## 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))## 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))
dendrogram_rjs creates a dendrogram.
dendrogram_rjs(data, metadata = NULL, method = "complete", cex = 1, plot = TRUE, jupyter = FALSE, dir = tempdir())dendrogram_rjs(data, metadata = NULL, method = "complete", cex = 1, plot = TRUE, jupyter = FALSE, dir = tempdir())
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. |
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.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.
## 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) }## 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) }
densityplot_rjs creates density plots.
densityplot_rjs(data, xlab = "", ylab = "", cex = 1, plot = TRUE, jupyter = FALSE, dir = tempdir())densityplot_rjs(data, xlab = "", ylab = "", cex = 1, plot = TRUE, jupyter = FALSE, dir = tempdir())
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. |
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.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.
## 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") }## 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") }
genomemap_rjs creates an interactive genome map.
genomemap_rjs(assembly, track = NULL, plot = TRUE, jupyter = FALSE, dir = tempdir())genomemap_rjs(assembly, track = NULL, plot = TRUE, jupyter = FALSE, dir = tempdir())
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 |
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. |
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).
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.
## 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 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) }
genomemap_rjs or manhattan_rjs.getAssemblyFromFasta create assemblies from a FASTA file for their use as parameter of genomemap_rjs or manhattan_rjs.
getAssemblyFromFasta(fasta)getAssemblyFromFasta(fasta)
fasta |
a "character" string representing the input Fasta file to be added in the genome browser. |
a data frame in BED format ready to use as an assembly in genomemap_rjs or manhattan_rjs.
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.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
## Live examples and full tutorial on https://rjsplot.usal.es## Live examples and full tutorial on https://rjsplot.usal.es
Length of human chromosomes based on GRCh37 assembly.
See https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13/.
A Data Frame containing cytobands of GRCh37 assembly.
See http://grch37.ensembl.org/Homo_sapiens/Location/Genome.
Length of human chromosomes based on GRCh38 assembly.
See https://www.ncbi.nlm.nih.gov/assembly/883148/.
A Data Frame containing cytobands of GRCh38 assembly.
See http://www.ensembl.org/Homo_sapiens/Location/Genome.
heatmap_rjs creates interactive heatmaps.
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)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)
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 ( |
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. |
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.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.
## 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") }## 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") }
hiveplot_rjs creates an interactive hive plot.
hiveplot_rjs(links, nodes = NULL, group = NULL, size = NULL, color = NULL, cex = 1, plot = TRUE, jupyter = FALSE, dir = tempdir())hiveplot_rjs(links, nodes = NULL, group = NULL, size = NULL, color = NULL, cex = 1, plot = TRUE, jupyter = FALSE, dir = tempdir())
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 |
size |
column name of |
color |
column name of |
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. |
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.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.
## 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 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") }
manhattan_rjs creates an interactive Manhattan plot.
manhattan_rjs(data, assembly, axisv, distv, cell = 1e+06, outliers = TRUE, ylab = "score", yscale = NULL, cex = 1, plot = TRUE, jupyter = FALSE, dir = tempdir())manhattan_rjs(data, assembly, axisv, distv, cell = 1e+06, outliers = TRUE, ylab = "score", yscale = NULL, cex = 1, plot = TRUE, jupyter = FALSE, dir = tempdir())
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: |
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 ( |
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. |
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.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.
## 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") }## 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") }
Length of human chromosomes based on NCBI36 assembly.
See https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.12/.
network_rjs creates an interactive network graph.
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())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())
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 |
linkLabel |
a vector giving the column of |
linkColor |
a vector giving the column of |
group |
a vector giving the column of |
size |
a vector giving the column of |
color |
a vector giving the column of |
label |
a vector giving the column of |
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. |
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.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.
## 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") }## 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") }
newInput object for R4web.newInput produce newInput object for R4web.
newInput(name, type = c("character","numeric","matrix","data.frame","factor"), default = "", levels = NULL, multi = FALSE)newInput(name, type = c("character","numeric","matrix","data.frame","factor"), default = "", levels = NULL, multi = FALSE)
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 |
multi |
boolean value which indicates if multiple selection are enabled for this input. It is described only for factor data |
Return a newInput object.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.
piechart_rjs produce interactive pie charts.
piechart_rjs(data, cex = 1, plot = TRUE, jupyter = FALSE, dir = tempdir())piechart_rjs(data, cex = 1, plot = TRUE, jupyter = FALSE, dir = tempdir())
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. |
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.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.
## 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 an interactive pie chart in a temporal directory of your local machine ## Live examples on https://rjsplot.usal.es if(interactive()){ piechart_rjs(VADeaths) }
R4web generate a PHP website which runs an R function.
R4web(...,fnfile,dir)R4web(...,fnfile,dir)
... |
one or more |
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. |
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.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.
report_rjs creates a report web page.
report_rjs(dir = "RJSreport") addCSS2report(report,css) addHTML2report(report,HTML) addParagraph2report(report,p) addPlot2report(report,plot,height=600) addImage2report(report,img)report_rjs(dir = "RJSreport") addCSS2report(report,css) addHTML2report(report,HTML) addParagraph2report(report,p) addPlot2report(report,plot,height=600) addImage2report(report,img)
dir |
a "character" string representing the directory where the report will be saved. |
report |
a RJSreport object produced by the function |
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. |
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.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.
Create interactive graphs with 'R'.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.
scatter3d_rjs generates an interactive 3D Scatter Plot.
scatter3d_rjs(x, y, z, color="#000", xlab = "x", ylab = "y", zlab = "z", plot = TRUE, jupyter = FALSE, dir = tempdir())scatter3d_rjs(x, y, z, color="#000", xlab = "x", ylab = "y", zlab = "z", plot = TRUE, jupyter = FALSE, dir = tempdir())
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. |
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.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.
## 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)") }## 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)") }
scatterplot_rjs generates an interactive Scatter Plot.
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())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())
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. |
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.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.
## 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$Species, xlab = "Sepal Width (cm)", ylab = "Sepal Length (cm)") }## Create an interactive Scatter plot in a temporal directory of your local machine ## Live examples on https://rjsplot.usal.es if(interactive()){ # Scatter plot creation scatterplot_rjs(iris$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)") }
surface3d_rjs generates an interactive 3D surface.
surface3d_rjs(x, color = "#fff", xlab = "x", ylab = "y", zlab = "z", plot = TRUE, jupyter = FALSE, dir = tempdir())surface3d_rjs(x, color = "#fff", xlab = "x", ylab = "y", zlab = "z", plot = TRUE, jupyter = FALSE, dir = tempdir())
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. |
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.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.
## 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")) }## 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")) }
symheatmap_rjs creates an interactive symetric heatmap.
symheatmap_rjs(links, nodes = NULL, group = NULL, label = NULL, cex = 1, plot = TRUE, jupyter = FALSE, dir = tempdir())symheatmap_rjs(links, nodes = NULL, group = NULL, label = NULL, cex = 1, plot = TRUE, jupyter = FALSE, dir = tempdir())
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 |
label |
a vector giving the column of |
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. |
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.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.
## 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") }## 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") }
tables_rjs produce interactive html tables of the given values.
tables_rjs(data, plot = TRUE, jupyter = FALSE, dir = tempdir())tables_rjs(data, plot = TRUE, jupyter = FALSE, dir = tempdir())
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. |
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.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.
## 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) }## 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) }
wordcloud_rjs creates a wordcloud.
wordcloud_rjs(data, plot = TRUE, jupyter = FALSE, dir = tempdir())wordcloud_rjs(data, plot = TRUE, jupyter = FALSE, dir = tempdir())
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. |
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.
David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/
The ‘RJSplot’ Website: https://rjsplot.usal.es
dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.
## 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) }## 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) }