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:

- Calculation of several correlation matrices corresponding to different link coefficients
- Clustering of variables using an unsupervised learning
- Supervised discretization of one or a couple of variables.

It also offers a customizable user interface, allowing to:

- visualize the links using a graph (the variables correspond to the nodes and the links correspond to the edges)
- show the distribution of each variable using its histogram or barplot
- visualize a link between a couple of variables using scatter plots, box plots, etc.

Available link coefficients are:

- Pearson’s r
- Spearman’s rho
- Kendall’s tau
- the Maximal Information Coefficient (MIC)
- the distance correlation
- the Maximal Normalized Mutual Information (MaxNMI)

`{r, echo=TRUE, eval=FALSE} install.packages("linkspotter")`

current development version from GitHub:

`{r, echo=TRUE, eval=FALSE} library(devtools) install_github("sambaala/linkspotter")`

Load the package:

`{r, echo=TRUE} library(linkspotter)`

Have a look at the documentation:

`{r, echo=TRUE, eval=FALSE} help(package="linkspotter")`

The examples are carried out using ‘iris’ data.

`{r, echo=TRUE} maxNMI(iris$Sepal.Length,iris$Petal.Length)`

`{r, echo=TRUE} corCouples<-multiBivariateCorrelation(iris) print(corCouples)`

The Pearson correlation matrix:

`{r, echo=TRUE} corMatrixPearson<-corCouplesToMatrix(x1_x2_val = corCouples[,c('X1','X2',"pearson")]) print(corMatrixPearson)`

The MaxNMI matrix:

`{r, echo=TRUE} corMatrixMaxNMI<-corCouplesToMatrix(x1_x2_val = corCouples[,c('X1','X2',"MaxNMI")]) print(corMatrixMaxNMI)`

`{r, echo=TRUE} cl<-clusterVariables(corMatrix = corMatrixMaxNMI) print(cl)`

`{r, echo=TRUE} linkspotterGraph(corDF = corCouples, variablesClustering = cl, corMethod = "pearson", minCor = 0.25, smoothEdges = FALSE, dynamicNodes = FALSE)`

`{r, echo=TRUE} linkspotterGraph(corDF = corCouples, variablesClustering = cl, corMethod = "MaxNMI", minCor = 0.25, smoothEdges = F, dynamicNodes = TRUE)`

`{r, echo=TRUE, eval=FALSE} linkspotterUI(dataset = iris, corDF = corCouples, variablesClustering = cl, appTitle = "Linkspotter example")`

Complete Linkspotter computation:

`{r, echo=TRUE} lsiris<-linkspotterComplete(iris)`

Complete Linkspotter computation from an external file:

`{r, echo=TRUE, eval=FALSE} lsiris<-linkspotterOnFile("iris.csv") summary(lsiris)`

`{r, echo=TRUE} summary(lsiris)`

Then launch the user interface (linkspotter shiny app) on port 8000 for example:

`{r, echo=TRUE, eval=FALSE} lsiris$launchShiny(options=list(port=8000))`

Help:

`{r, echo=TRUE, eval=FALSE} 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).

**Correlation coefficient**drop-down list : allows to choose the link coefficient to be visualized.**Minimum Correlation**cursor: allows to define the minimum link measurement (from 0 to 1) threshold necessary to plot a edge.**Interest variable**drop-down list: allows to choose a variable of interest. If a variable of interest is selected, a new cursor named**Minimum Correlation with interest variable**appears. It gives the possibility of defining a new minimum threshold of correlation specific to this variable of interest, in addition to the general threshold. The upper limit of this specific threshold is the global threshold.

**Highlight variable on click**: if checked, it is possible to focus on a node, by clicking on it or by selecting it from the drop-down list that appears.**Variable Clustering**: If checked, the nodes are colored according to the group to which they belong. If it is not checked, all nodes are blue.**Color Edges by correlation direction**: if checked, the edges are colored according to the direction of the correlation (blue for a positive correlation, red for a negative correlation and gray for NA) found between the two variables. The NA case corresponds to when at least one of the two variables is qualitative.**Smooth edges**: if checked, edges are allowed to bend as needed. Otherwise, they remain straight.**Dynamic nodes stabilization**: if checked, the graph is repositioned according to the graph stabilization algorithm after each movement by the user.**Re-stabilize**: button that allows to re-stabilize the graph (centering and redistribution of the nodes on plane in “almost optimal” way)

**nb. observations**: the number of entries in the dataset**nb. variables**: the number of variables in the dataset**nb. couples**: the number of couples**nb. current edges**: the current number of edges plotted according to the chosen thresholds

It produces the following:

Its type depends on the nature of the corresponding link:

- Quantitative variable vs quantitative variable: a point cloud
- Variable quantitative vs qualitative variable: a boxplot
- Qualitative variable vs qualitative variable: not yet treated

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:

- Quantitative variable: a histogram
- Qualitative variable: a bar graph

Its type depends on the nature of the variable:

- Quantitative variable: a table containing the min, 1st quartile, median, mean, 3rd quartile and max of the variable.
- Qualitative variable: a table containing the frequency of each modality of the variable.

This tab displays 2 tables:

- A correlation matrix corresponding to the selected correlation coefficient
- A table indicating the group which each variable is assigned to after by the clustering.

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’, ‘shinybusy’, ‘visNetwork’, ‘rAmCharts’ and ‘ggplot2’.