Create a sankey plot — sankeyPlot • GiottoVisuals

Create a sankey plot. Pulls from information metadata if giotto object is provided. Simple 1 to 1 sankeys can be generated from a single spatial unit and feature type using the spat_unit, feat_type, meta_type, cols, and (optionally) idx params. More complex and cross spatial unit/feature type sankeys can be set up using the sankey_plan param which accepts a giottoSankeyPlan object.
Also possible to directly use data.frames or lists of data.frames and giottoPolygon objects. See usage section and examples.

Usage

# S4 method for class 'giotto,giottoSankeyPlan'
sankeyPlot(
  x,
  y,
  meta_type = c("cell", "feat"),
  focus_names = NULL,
  unfocused_color = FALSE,
  ...
)

# S4 method for class 'giotto,character'
sankeyPlot(
  x,
  y,
  spat_unit = NULL,
  feat_type = NULL,
  meta_type = c("cell", "feat"),
  idx = NULL,
  focus_names = NULL,
  unfocused_color = FALSE,
  ...
)

# S4 method for class 'data.frame,missing'
sankeyPlot(x, focus_names = NULL, unfocused_color = FALSE, ...)

# S4 method for class 'list,missing'
sankeyPlot(x, focus_names = NULL, unfocused_color = FALSE, ...)

# S4 method for class 'giottoPolygon,giottoPolygon'
sankeyPlot(x, y, focus_names = NULL, unfocused_color = FALSE, ...)

Arguments

x

data source (gobject, data.frame-like object with relations between the first two cols provided, or giottoPolygon)

y

giottoSankeyPlan object or character vector referring to source and target columns in metadata if x is a gobject. Can also be missing or a second giottoPolygon (see usage section)

meta_type

whether to use 'cell' (cell) or 'feat' (feature) metadata

focus_names

character vector of node names to display. Others will be omitted.

unfocused_color

whether to color nodes that are not focused on.

...

Arguments passed on to networkD3::sankeyNetwork

Value: character string naming the variable in the Links data frame for how far away the nodes are from one another.
NodeGroup: character string specifying the node groups in the Nodes. Used to color the nodes in the network.
LinkGroup: character string specifying the groups in the Links. Used to color the links in the network.
units: character string describing physical units (if any) for Value
colourScale: character string specifying the categorical colour scale for the nodes. See https://github.com/d3/d3/blob/master/API.md#ordinal-scales.
fontSize: numeric font size in pixels for the node text labels.
fontFamily: font family for the node text labels.
nodeWidth: numeric width of each node.
nodePadding: numeric essentially influences the width height.
margin: an integer or a named list/vector of integers for the plot margins. If using a named list/vector, the positions top, right, bottom, left are valid. If a single integer is provided, then the value will be assigned to the right margin. Set the margin appropriately to accomodate long text labels.
height: numeric height for the network graph's frame area in pixels.
width: numeric width for the network graph's frame area in pixels.
iterations: numeric. Number of iterations in the diagramm layout for computation of the depth (y-position) of each node. Note: this runs in the browser on the client so don't push it too high.
sinksRight: boolean. If TRUE, the last nodes are moved to the right border of the plot.

spat_unit

spatial unit of metadata

feat_type

feature type of metadata

idx

table subset index for 1 to 1 comparisons

Value

sankey plot

Examples

x <- data.frame(
    col1 = c("a", "a", "b"),
    col2 = c("1", "2", "2")
)
sankeyPlot(x)
#> Error: package 'networkD3' is not yet installed
#> 
#>  To install:
#> install.packages(c("networkD3"))

y <- data.frame(
    col1 = "1",
    col2 = c("A", "B", "C")
)

# combine data.frames of relations
# rbind: note that node "1" is mapped the same for x and y
sankeyPlot(rbind(x, y), fontSize = 20)
#> Error: package 'networkD3' is not yet installed
#> 
#>  To install:
#> install.packages(c("networkD3"))

# list: note that node "1" is now considered a different node between x and y
sankeyPlot(list(x, y), fontSize = 20)
#> Error in loadNamespace(x): there is no package called ‘networkD3’

# focus on specific nodes/names
sankeyPlot(rbind(x, y), fontSize = 20, focus_names = c("a", "1", "B"))
#> Error: package 'networkD3' is not yet installed
#> 
#>  To install:
#> install.packages(c("networkD3"))

g <- GiottoData::loadGiottoMini("vizgen")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#>  active environment : '/usr/bin/python3'
#>  python version : 3.12
# with giottoSankeyPlan
leiden <- sankeySet(
    spat_unit = "aggregate",
    feat_type = "rna",
    col = "leiden_clus"
)
louvain <- sankeySet(
    spat_unit = "aggregate",
    feat_type = "rna",
    col = "louvain_clus"
)
# place defined sets into same object
plan <- leiden + louvain
# assign relationships to compare
sankeyRelate(plan) <- c(0, 1)
sankeyPlot(g, plan)
#> Error: package 'networkD3' is not yet installed
#> 
#>  To install:
#> install.packages(c("networkD3"))

# with single set of metadata
GiottoClass::activeSpatUnit(g) <- "aggregate"
sankeyPlot(g, c("louvain_clus", "leiden_clus"))
#> Error: package 'networkD3' is not yet installed
#> 
#>  To install:
#> install.packages(c("networkD3"))