makeRiver: Create a new riverplot object

In riverplot: Sankey or Ribbon Plots

Description

Create a new riverplot object

Usage

makeRiver(
  nodes,
  edges,
  node_labels = NULL,
  node_xpos = NULL,
  node_ypos = NULL,
  styles = NULL,
  node_styles = NULL,
  edge_styles = NULL,
  default_style = NULL
)

Arguments

nodes	Data frame with node ID's, positions and optionally other information
edges	A named list or a data frame specifying the edges between the nodes.
node_labels	A named character vector of labels for the nodes
node_xpos	A named vector of numeric values specifying the horizontal positions on the plot.
node_ypos	A named vector of numeric values specifying the vertical positions on the plot.
styles	A named list specifying the styles for the nodes and edges
node_styles	Deprecated
edge_styles	Deprecated
default_style	list containing style information which is applied to every node and every edge

Details

Functions to create a new object of the riverplot class from the provided data.

makeRiver creates a plot from an object which specifies the graph directly, i.e. all nodes, their horizontal positions on the plot, provided styles etc. See sections below for detailed explanations.

Value

A riverplot object which can directly be plotted.

Structure of the riverplot objects

A riverplot object is a list with the following entries:

nodes

A data frame specifying the nodes, containing at least the columns "ID" and "x" (horizontal position of the node). Optionally, it can also contain columns "labels" (the labels to display) and "y" (vertical position of the node on the plot)

edges

A data frame specifying the edges and graph topology, containing at least the columns "ID", "N1", "N2" and "Value", specifying, respectively, the ID of the edge, the parent node, the child node, and the size of the edge.

styles

A named list of styles. Names of this list are the node or edge IDs. Values are styles specifying the style of the given node or edge (see below).

Whether or not the list used to plot is exactly of class riverplot-class does not matter as long as it has the correct contents. The makeRiver function is here are for the convenience of checking that this is the case and converting information in different formats.

Generating riverplot objects

To generate and fool-proof riverplot objects, you can use the makeRiver function. This functions allows a number of ways of specifying the node and edge information.

Nodes can be specified as a character vector (simply listing the nodes) or as a data frame.

• character vector: in this case, you also need to provide the node_xpos argument to specify the horizontal positions of the nodes.

• data frame: the data frame must have at least a column called "ID"; the horizontal position can be specified either with node_xpos argument or by column "x" in the data frame. Optionally, the data frame can include columns "labels" and "y" (vertical positions of the node). Any NA values are ignored (not entered into the riverplot project). Additionaly, the data frame may contain style information.

Edges / graph topology can be specified in one of two objects: either a named list, or a data frame:

• you can supply a named list with edges of the graph. The name of each element is the name of the outgoing (parental) node. Each element is a named list; the names of the list are the names of the incoming (child) node IDs; the values are the width of the edge between the outgoing and incoming nodes.

• Alternatively, you can provide the edges as a data frame. Each row corresponds to an edge, and the data frame must have the following columns:

  N1

  The ID of the first node

  N2

  The ID of the second node

  Value

  The width of the edge between N1 and N2

  If an ID column is absent, it will be generated from N1 and N2 by joining the N1 and N2 ID's with the "->" string. Additionaly, the data frame may contain style information. Any NA values are ignored (not entered into the riverplot object).

Riverplot styles

Styles are lists containing attributes (such as "col" for color or "nodestyle") and values. There is no real difference between node and edge styles, except that some attributes only apply to nodes or edges. See riverplot-styles for more information on style attributes.

When makeRiver generates the riverplot object, it combines style information from the following sources in the following order:

• parameter default_style is a style applied to all nodes and edges

• if the parameter nodes and/or edges is a data frame, it may include columns with names corresponding to style attributes. For example, a column called "col" will contain the color attribute for any nodes / edges. NA values in these columns are ignored.

• styles is a lists of styles, with names corresponding to node IDs or edge IDs, which will replace any previously specified styles.

Author(s)

January Weiner

Examples

nodes <- c( LETTERS[1:3] )
edges <- list( A= list( C= 10 ), B= list( C= 10 ) )
r <- makeRiver( nodes, edges, node_xpos= c( 1,1,2 ),
  node_labels= c( A= "Node A", B= "Node B", C= "Node C" ),
  node_styles= list( A= list( col= "yellow" )) )
plot( r )

# equivalent form:
nodes <- data.frame( ID= LETTERS[1:3],
               x= c( 1, 1, 2 ),
               col= c( "yellow", NA, NA ),
               labels= c( "Node A", "Node B", "Node C" ),
               stringsAsFactors= FALSE )
r <- makeRiver( nodes, edges )
plot( r )
# all nodes but "A" will be red:
r <- makeRiver( nodes, edges, default_style= list( col="red" ) )
plot( r )
# overwrite the node information from "nodes":
r <- makeRiver( nodes, edges, node_styles= list( A=list( col="red" ) ) )
plot( r )

Example output

--------------
Default style:
-----------
$nodestyle
[1] "regular"

$col
[1] "grey"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle"
--------------
[1] "checking edges"
[1] "adding mid points"
Updated styles:
$A
$col
[1] "yellow"

$nodestyle
[1] "regular"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle"

$B
$nodestyle
[1] "regular"

$col
[1] "grey"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle"

$C
$nodestyle
[1] "regular"

$col
[1] "grey"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle"

$`A->C`
$nodestyle
[1] "regular"

$col
[1] "grey"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle"

$`B->C`
$nodestyle
[1] "regular"

$col
[1] "grey"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle"

--------------
[1] "calculating sizes"
$lefts
 A  B  C 
 0  0 20 

$rights
 A  B  C 
10 10  0 

$sizey
 A  B  C 
10 10 20 

[1] "calculating positions"
[1] 2
  ID x labels
A  A 1 Node A
B  B 1 Node B
C  C 2 Node C
[1] "done"
[1] "drawing edges"
[1] "drawing nodes"
--------------
Default style:
-----------
$nodestyle
[1] "regular"

$col
[1] "grey"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle"
--------------
[1] "checking edges"
[1] "adding mid points"
Updated styles:
$A
$col
       A 
"yellow" 

$nodestyle
[1] "regular"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle"

$B
$nodestyle
[1] "regular"

$col
[1] "grey"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle"

$C
$nodestyle
[1] "regular"

$col
[1] "grey"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle"

$`A->C`
$nodestyle
[1] "regular"

$col
[1] "grey"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle"

$`B->C`
$nodestyle
[1] "regular"

$col
[1] "grey"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle"

--------------
[1] "calculating sizes"
$lefts
 A  B  C 
 0  0 20 

$rights
 A  B  C 
10 10  0 

$sizey
 A  B  C 
10 10 20 

[1] "calculating positions"
[1] 2
  ID x    col labels
A  A 1 yellow Node A
B  B 1   <NA> Node B
C  C 2   <NA> Node C
[1] "done"
[1] "drawing edges"
[1] "drawing nodes"
--------------
Default style:
-----------
$nodestyle
[1] "regular"

$col
[1] "grey"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle"
--------------
[1] "checking edges"
[1] "adding mid points"
Updated styles:
$A
$col
       A 
"yellow" 

$nodestyle
[1] "regular"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle"

$B
$col
[1] "red"

$nodestyle
[1] "regular"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle" "riverplotStyle"

$C
$col
[1] "red"

$nodestyle
[1] "regular"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle" "riverplotStyle"

$`A->C`
$col
[1] "red"

$nodestyle
[1] "regular"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle" "riverplotStyle"

$`B->C`
$col
[1] "red"

$nodestyle
[1] "regular"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle" "riverplotStyle"

--------------
[1] "calculating sizes"
$lefts
 A  B  C 
 0  0 20 

$rights
 A  B  C 
10 10  0 

$sizey
 A  B  C 
10 10 20 

[1] "calculating positions"
[1] 2
  ID x    col labels
A  A 1 yellow Node A
B  B 1   <NA> Node B
C  C 2   <NA> Node C
[1] "done"
[1] "drawing edges"
[1] "drawing nodes"
--------------
Default style:
-----------
$nodestyle
[1] "regular"

$col
[1] "grey"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle"
--------------
[1] "checking edges"
[1] "adding mid points"
Updated styles:
$A
$col
[1] "red"

$nodestyle
[1] "regular"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle"

$B
$nodestyle
[1] "regular"

$col
[1] "grey"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle"

$C
$nodestyle
[1] "regular"

$col
[1] "grey"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle"

$`A->C`
$nodestyle
[1] "regular"

$col
[1] "grey"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle"

$`B->C`
$nodestyle
[1] "regular"

$col
[1] "grey"

$srt
[1] "90"

$lty
[1] 1

$textcol
[1] "black"

$textcex
[1] 1

$edgecol
[1] "gradient"

$edgestyle
[1] "sin"

attr(,"class")
[1] "list"           "riverplotStyle"

--------------
[1] "calculating sizes"
$lefts
 A  B  C 
 0  0 20 

$rights
 A  B  C 
10 10  0 

$sizey
 A  B  C 
10 10 20 

[1] "calculating positions"
[1] 2
  ID x    col labels
A  A 1 yellow Node A
B  B 1   <NA> Node B
C  C 2   <NA> Node C
[1] "done"
[1] "drawing edges"
[1] "drawing nodes"

riverplot documentation built on Jan. 22, 2021, 5:09 p.m.