Linkspotter is a package of the R software that mainly allows to calculate and visualize using a graph all the bivariate links of a dataset.
Its main features are:
It also offers a customizable user interface, allowing to:
Available link coefficients are:
library(devtools) install_github("sambaala/linkspotter")
Behind a proxy:
library(devtools) library(httr) set_config( use_proxy(url="<my_proxy>", port=<my_proxy_port>) ) install_github("sambaala/linkspotter")
Load the package:
library(linkspotter)
Take a look at the documentation:
help(package="linkspotter")
The examples are carried out using "iris" data.
maxNMI(iris$Sepal.Length,iris$Petal.Length)
corCouples<-multiBivariateCorrelation(iris) print(corCouples)
The Pearson correlation matrix:
corMatrixPearson<-corCouplesToMatrix(x1_x2_val = corCouples[,c('X1','X2',"pearson")]) print(corMatrixPearson)
The MaxNMI matrix:
corMatrixMaxNMI<-corCouplesToMatrix(x1_x2_val = corCouples[,c('X1','X2',"MaxNMI")]) print(corMatrixMaxNMI)
cl<-clusterVariables(corMatrix = corMatrixMaxNMI) print(cl)
linkspotterGraph(corDF = corCouples, variablesClustering = cl, corMethod = "pearson", minCor = 0.25, smoothEdges = FALSE, dynamicNodes = FALSE)
linkspotterGraph(corDF = corCouples, variablesClustering = cl, corMethod = "MaxNMI", minCor = 0.25, smoothEdges = F, dynamicNodes = TRUE)
linkspotterUI(dataset = iris, corDF = corCouples, variablesClustering = cl, appTitle = "Linkspotter example")
Complete Linkspotter computation:
lsiris<-linkspotterComplete(iris)
Complete Linkspotter computation from an external file:
lsiris<-linkspotterOnFile("iris.csv") summary(lsiris)
summary(lsiris)
Then launch the user interface using:
lsiris$launchShiny()
Help:
help(linkspotterComplete)
The variables correspond to the nodes and their links correspond to the edges. Node color depends on the clustering. Edge color depends on the correlation direction quantitative couples (blue: positive correlation, red: negative correlation).
It produces the following:
Its type depends on the nature of the corresponding link:
It displays all the measurements calculated for the link corresponding to the clicked edge. When at least one of the variables is qualitative, only the MaxNMI has a value.
It produces the following:
Its type depends on the nature of the corresponding variable:
Its type depends on the nature of the variable:
This tab displays 2 tables:
The Correlation coefficient option allows you to choose the coefficient of correlation to be considered among those calculated initially.
Linkspotter uses and combine features coming from several other R packages, namely infotheo, minerva, energy, mclust, shiny, visNetwork, rAmCharts and ggplot2.
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