Create a sankey plot

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 giotto,giottoSankeyPlan
sankeyPlot(
  x,
  y,
  meta_type = c("cell", "feat"),
  focus_names = NULL,
  unfocused_color = FALSE,
  ...
)

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

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

# S4 method for 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
#> /home/runner/work/_temp/Library/GiottoData/Mini_datasets/Vizgen/VizgenObject/Features/rna_feature_spatVector.shp
#> rna
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> aggregate_spatInfo_spatVector.shp z0_spatInfo_spatVector.shp
#>  z1_spatInfo_spatVector.shp
#> aggregate
#> z0
#> z1
#> 
#> 3.2 read Giotto spatial centroid information
#> aggregate
#> z0
#> z1
#> 
#> 3.3 read Giotto spatial overlap information
#> rna_aggregate_spatInfo_spatVectorOverlaps.shp
#>  rna_z0_spatInfo_spatVectorOverlaps.shp rna_z1_spatInfo_spatVectorOverlaps.shp
#> poly_ID feat_ID feat_ID_uniq stack
#> aggregate and rna
#> poly_ID feat_ID feat_ID_uniq
#> z0 and rna
#> poly_ID feat_ID feat_ID_uniq
#> z1 and rna
#> 
#> 4. read Giotto image information
#> 
#> no external python path or giotto
#>  environment was specified, will check if a
#>  default python path is available
#> 
#> A default python path was found: /usr/bin/python3 and will be used
#>  If this is not the correct python path, either
#> 
#> 1. use installGiottoEnvironment() to install
#>  a local miniconda python environment along with required modules
#> 
#> 2. provide an existing python path to
#>  python_path to use your own python path which has all modules
#>  installed
#> Set options("giotto.use_conda" = FALSE) if
#>  python functionalities are not needed
# 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"))