visHclust: Visualize Hierarchical cluster analysis.

In datastorm-open/visNetwork: Network Visualization using 'vis.js' Library

Visualize Hierarchical cluster analysis.

Description

Visualize Hierarchical cluster analysis hclust. This function compute distance using dist, and Hierarchical cluster analysis using hclust (from stats package or flashClust if installed), and render the tree with visNetwork, adding informations. Can also be called on a hclust or dist object. Needed packages : sparkline (graphics on tooltip), ggraph, igraph, flashClust

Usage

visHclust(object, ...)

## Default S3 method:
visHclust(object, ...)

## S3 method for class 'data.frame'
visHclust(
  object,
  main = "",
  submain = "",
  footer = "",
  distColumns = NULL,
  distMethod = "euclidean",
  hclustMethod = "complete",
  cutree = 0,
  tooltipColumns = 1:ncol(object),
  colorEdges = "black",
  colorGroups = substr(rainbow(cutree), 1, 7),
  highlightNearest = TRUE,
  horizontal = FALSE,
  minNodeSize = 50,
  maxNodeSize = 200,
  nodesPopSize = TRUE,
  height = "600px",
  width = "100%",
  export = TRUE,
  ...
)

## S3 method for class 'dist'
visHclust(
  object,
  data = NULL,
  main = "",
  submain = "",
  footer = "",
  cutree = 0,
  hclustMethod = "complete",
  tooltipColumns = if (!is.null(data)) {     1:ncol(data) } else {     NULL },
  colorEdges = "black",
  colorGroups = substr(rainbow(cutree), 1, 7),
  highlightNearest = TRUE,
  horizontal = FALSE,
  minNodeSize = 50,
  maxNodeSize = 200,
  nodesPopSize = TRUE,
  height = "600px",
  width = "100%",
  export = TRUE,
  ...
)

## S3 method for class 'hclust'
visHclust(
  object,
  data = NULL,
  main = "",
  submain = "",
  footer = "",
  cutree = 0,
  tooltipColumns = if (!is.null(data)) {     1:ncol(data) } else {     NULL },
  colorEdges = "black",
  colorGroups = substr(rainbow(cutree), 1, 7),
  highlightNearest = TRUE,
  horizontal = FALSE,
  minNodeSize = 50,
  maxNodeSize = 200,
  nodesPopSize = TRUE,
  height = "600px",
  width = "100%",
  export = TRUE,
  ...
)

Arguments

object	hclust | dist | data.frame.
...	Don't use
main	Title. See visNetwork
submain	Subtitle. See visNetwork
footer	Footer. See visNetwork
distColumns	numeric, indice of columns used for compute distance. If NULL (default), keep all numeric and integer columns. If Not NULL, keep only numeric and integer columns
distMethod	character, the distance measure to be used for dist function. Default to 'euclidean'.
hclustMethod	character, the agglomeration method to be used for hclust function. Default to 'complete'.
cutree	numeric or integer, desired number of groups. Default to 0.
tooltipColumns	numeric, adding mini-graphics in tooltips using sparkline ? Indice of columns used in tooltip. All by default. So, we add boxplot / pie focus on sub-population vs all population using sparkline package. NULL to disable.
colorEdges	character, color of edges. Default to 'black'.
colorGroups	character, color for group in hexa ("#00FF00"). Default rainbow.
highlightNearest	boolean, highlight sub-tree on click ? Default to TRUE.
horizontal	boolean, default to FALSE
minNodeSize	numeric, in case of nodesPopSize, minimum size of a node. Default to 50. Else minNodeSize + maxNodeSize / 2.
maxNodeSize	numeric, in case of nodesPopSize, maximum size of a node. Default to 200. Else minNodeSize + maxNodeSize / 2.
nodesPopSize	boolean, nodes sizes depends on population ? Default to TRUE.
height	character, default to "600px"
width	character, default to "100%"
export	boolean, add button for export. Default to TRUE
data	data.frame, data.frame with data. Only for hclust or dist object.

Examples

## Not run: 

#--------------
# data.frame
#--------------

# default call on data.frame
visHclust(iris, cutree = 3, colorEdges = "red")

# update some parameters
visHclust(iris, cutree = 3, tooltipColumns = c(1, 5),
  colorGroups = c("red", "blue", "green"), horizontal = TRUE)
  
# no graphics on tooltip
visHclust(iris, cutree = 3, tooltipColumns = NULL,
  main = "Hclust on iris")
  
# Title(s)
visHclust(iris, cutree = 3,  main ="My_title",
          submain = "My_sub_title", footer = "My_footer")
          
# Export
visHclust(iris, cutree = 3, export = TRUE)


# update group / individual nodes
visHclust(iris, cutree = 8) %>% 
 visGroups(groupname = "group", color ="black", 
   shape = "triangleDown", size = 75)  %>% 
 visGroups(groupname = "individual", 
   font = list(size = 150),
   color = list(background = "white", border = "purple", 
            highlight = "#e2e9e9", hover = "orange"), shape = "box") 

#--------------
# dist
#--------------

# without adding data & info in tooltip
visHclust(dist(iris[,1:4]), cutree = 3)
  
# adding data & info in tooltip
visHclust(dist(iris[,1:4]), cutree = 3, data = iris)

#--------------
# hclust
#--------------

# without adding data & info in tooltip
visHclust(hclust(dist(iris[,1:4])), cutree = 3)
  
# adding data & info in tooltip
visHclust(hclust(dist(iris[,1:4])), cutree = 3, data = iris) 
    

## End(Not run)

datastorm-open/visNetwork documentation built on Dec. 3, 2022, 8:50 p.m.