explor is an R package to allow interactive exploration of multivariate analysis results.
For now on, the following analyses are supported :
Analysis | Function | Package | Notes ------------- | ------------- | ---------- | -------- Principal component analysis | PCA | FactoMineR | - Correspondance analysis | CA | FactoMineR | - Multiple correspondence analysis | MCA | FactoMineR | - Principal component analysis | dudi.pca | ade4 | Qualitative supplementary variables are ignored Correspondance analysis | dudi.coa | ade4 | - Multiple correspondence analysis | dudi.acm | ade4 | Quantitative supplementary variables are ignored Specific Multiple Correspondance Analysis | speMCA | GDAtools | Supplementary variables are not supported Multiple Correspondance Analysis | mca | MASS | Quantitative supplementary variables are not supported Principal Component Analysis | princomp | stats | Supplementary variables are ignored Principal Component Analysis | prcomp | stats | Supplementary variables are ignored
The philosophy behind
explor is to only be an exploration interface which doesn't really do anything by itself : analysis and computations are made in your R script, and
explor only helps you visualizing the results. As such it can not disrupt code execution and reproducibility.
For each type of analysis,
explor launches a
shiny interactive Web interface which is displayed inside RStudio or in your system Web browser. This interface provides a series of tabs with interactive data and graphics.
These data and graphics are displayed with several "interactive" features. Numerical results are shown as dynamic tables which are sortable and searchable thanks to the
DT package. Most graphics are generated with the
scatterD3 package which provides the following features :
Usage is very simple : you just apply the
explor() function to the result object of one of the supported analysis functions.
To visualize and explore these functions results, just pass the result object
Here is an example for a sample PCA with
data(USArrests) pca <- princomp(USArrests, cor = TRUE) explor(pca)
explor supports the visualization of supplementary individuals whose scores
have been computed with
predict. You just have to add them as a
element to your result object.
Here is an example with
pca <- prcomp(USArrests[6:50,], scale. = TRUE) pca$supi <- predict(pca, USArrests[1:5,]) explor(pca)
explor() also supports qualitative supplementary variables.
You must include their predicted coordinates to a
supv element. It's also
best to manually add row names to the
supidata, if any :
library(MASS) mca <- MASS::mca(farms[4:20, 2:4], nf = 11) supi_df <- farms[1:3, 2:4] supi <- predict(mca, supi_df, type="row") rownames(supi) <- rownames(supi_df) mca$supi <- supi mca$supv <- predict(mca, farms[4:20, 1, drop=FALSE], type="factor") explor(mca)
Note that the results of these three functions are quite limited : they provide variables and individuals coordinates, but no contributions or squared cosinus.
FactoMineR functions should work "out of the box". Just pass the result object to
Example with a principal correspondence analysis from
library(FactoMineR) data(decathlon) pca <- PCA(decathlon[,1:12], quanti.sup = 11:12) explor(pca)
Example with a simple correspondence analysis from
data(children) res.ca <- CA(children, row.sup = 15:18, col.sup = 6:8) explor(res.ca)
Example with a multiple correspondence analysis from
library(FactoMineR) data(hobbies) mca <- MCA(hobbies[1:1000, c(1:8,21:23)], quali.sup = 9:10, quanti.sup = 11, ind.sup = 1:100) explor(mca)
ade4 functions should also work by directly passing the object result to
For example, to visualize a simple PCA results :
library(ade4) data(deug) pca <- dudi.pca(deug$tab, scale = TRUE, scannf = FALSE, nf = 5) explor(pca)
There's a bit more work to be done if you want to display supplementary elements, as
ade4 don't include them directly in the results analysis.
For a principal component analysis, you have to compute supplementary individuals (resp. variables) results with
supcol) and add them manually as a
supv) element of your result object.
Here is an example of how to do this :
data(deug) d <- deug$tab sup_var <- d[-(1:10), 8:9] sup_ind <- d[1:10, -(8:9)] pca <- dudi.pca(d[-(1:10), -(8:9)], scale = TRUE, scannf = FALSE, nf = 5) ## Supplementary individuals supi <- suprow(pca, sup_ind) pca$supi <- supi$lisup ## Supplementary variables supv <- supcol(pca, dudi.pca(sup_var, scale = TRUE, scannf = FALSE)$tab) pca$supv <- supv$cosup explor(pca)
You have to do the same thing for supplementary elements in a multiple correspondence analysis :
data(banque) d <- banque[-(1:100),-(19:21)] ind_sup <- banque[1:100, -(19:21)] var_sup <- banque[-(1:100),19:21] acm <- dudi.acm(d, scannf = FALSE, nf = 5) ## Supplementary variables acm$supv <- supcol(acm, dudi.acm(var_sup, scannf = FALSE, nf = 5)$tab)$cosup ## Supplementary individuals acm$supi <- suprow(acm, ind_sup)$lisup explor(acm)
For simple correspondence analysis, you can add supplementary rows or columns by adding their coordinates to
supc elements of your result object :
data(bordeaux) tab <- bordeaux row_sup <- tab[5,-4] col_sup <- tab[-5,4] coa <- dudi.coa(tab[-5,-4], nf = 5, scannf = FALSE) coa$supr <- suprow(coa, row_sup)$lisup coa$supc <- supcol(coa, col_sup)$cosup explor(coa)
GDAtools functions should also work by directly passing the object result to
For example, to visualize a
speMCA results :
library(GDAtools) data(Music) mca <- speMCA(Music[,1:5],excl=c(3,6,9,12,15)) explor(mca)
To display supplementary individuals, you have to compute their data with the
indsup function, and add them manually as a
supi element of your result object.
Here is an example :
library(GDAtools) data(Music) mca <- speMCA(Music[3:nrow(Music),1:5],excl=c(3,6,9,12,15)) mca$supi <- indsup(mca,Music[1:2,1:5]) explor(mca)
explor provides two different ways to export the displayed plots.
To save the displayed plot as an SVG file, click on the Export to SVG button in the bottom of the left sidebar, or choose Export to SVG in the gear menu.
SVG is a vector graphics format, editable with softwares like Inkscape.
This SVG export may cause issues when used inside RStudio. As a workaround, you can open
explor in a browser (with Open in Browser icon) before exporting.
Another way is to get the R code which allows to generate the current plot. This code can then be used in a script or a Rmarkdown document.
To do this, click on the Get R code button on the bottom of the left sidebar. A modal dialog should show up with the R code that you can then copy/paste.
Please note that this R code keeps track of the current plot zooming, but not of any custom label positioning. If you want to keep those, you have to first save them in a CSV file with Export labels positions gear menu entry. Then, in your R script, read this file in an object with
read.csv and pass this object to the
export_labels_positions argument in the generated code :
labels <- read.csv("position_labels.csv") res <- explor::prepare_results(mca) explor::MCA_var_plot(res, xax = 1, yax = 2, var_sup = TRUE, , var_lab_min_contrib = 0, col_var = "Variable", symbol_var = "Type", size_var = NULL, size_range = c(10, 300), labels_size = 10, point_size = 56, transitions = TRUE, labels_positions = labels)
explor is quite a young package, so there certainly are bugs or problems. Thanks for reporting them by mail or by opening an issue on GitHub
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