do_AlluvialPlot() | Flow between categories

Alluvial plots visualize how cells flow between categorical groups—for example, how cluster assignments change across conditions, time points, or annotation methods. Built on the ggalluvial package.

Basic usage

Visualize how cells in clusters map to cell types:

p <- SCpubr::do_AlluvialPlot(sample = sample,
                             first_group = "Annotation",
                             last_group = "subtype")
p

Multiple intermediate groups

Add intermediate nodes between start and end:

p <- SCpubr::do_AlluvialPlot(
  sample        = sample,
  first_group   = "technology",
  middle_groups = c("Annotation"),
  last_group    = "subtype"
)
p

Color by group

Control which group determines the flow colors:

# Color by last group (default)
p <- SCpubr::do_AlluvialPlot(sample = sample,
                             first_group = "Annotation",
                             last_group = "subtype",
                             fill.by = "subtype")

p

# Color by first group 
p <- SCpubr::do_AlluvialPlot(sample = sample,
                             first_group = "Annotation",
                             last_group = "subtype",
                             fill.by = "Annotation")

p

Stratum customization

Fill stratum based on flow

p <- SCpubr::do_AlluvialPlot(sample = sample,
                             first_group = "Annotation",
                             last_group = "subtype",
                             stratum.fill.conditional = TRUE)
p

Custom stratum appearance

p <- SCpubr::do_AlluvialPlot(sample = sample,
                             first_group = "Annotation",
                             last_group = "subtype",
                             stratum.fill = "grey90",
                             stratum.color = "black",
                             stratum.width = 1/4)
p

Flow styles

Use geom_flow (alternative rendering)

p <- SCpubr::do_AlluvialPlot(sample = sample,
                             first_group = "Annotation",
                             last_group = "subtype",
                             use_geom_flow = TRUE)
p

Curve types

# Available: linear, cubic, quintic, sine, arctangent, sigmoid, xspline
p <- SCpubr::do_AlluvialPlot(sample = sample,
                             first_group = "Annotation",
                             last_group = "subtype",
                             curve_type = "xspline")
p

Use labels

Replace stratum boxes with text labels:

p <- SCpubr::do_AlluvialPlot(sample = sample,
                             first_group = "Annotation",
                             last_group = "subtype",
                             use_labels = TRUE,
                             repel = TRUE)
p

Parameter reference

Note

For parameters shared across many functions (color palettes, typography, legend styling), see Shared features.

Core parameters

Parameter Description Default
first_group Starting categorical variable —
last_group Ending categorical variable —
middle_groups Intermediate variables NULL
fill.by Variable to color flows by last_group

Stratum appearance

Parameter Description Default
stratum.fill Stratum fill color "white"
stratum.color Stratum border color "black"
stratum.width Stratum width 1/3
stratum.fill.conditional Match stratum to flow color FALSE

Flow appearance

Parameter Description Default
use_geom_flow Use alternative flow rendering FALSE
alluvium.color Flow border color "white"
curve_type Curve shape "sigmoid"

Labels

Parameter Description Default
use_labels Show text labels instead of boxes FALSE
repel Repel overlapping labels FALSE
label.color Label text color "black"

See also