DimPlotAtomic: Atomic Dimension Reduction Plot without splitting the data
In plotthis: High-Level Plotting Built Upon 'ggplot2' and Other Plotting Packages

DimPlotAtomic

R Documentation

Atomic Dimension Reduction Plot without splitting the data

Description

Core implementation for dimension reduction visualisation. This is the internal workhorse dispatched by both DimPlot() (group-based) and FeatureDimPlot() (continuous feature expression). It renders a 2D scatter plot of ordination axes with extensive annotation capabilities, and automatically delegates to DimPlotAtomic3D() for interactive 3D plots when three dims are provided.

The function supports two primary colouring modes:

group_by — discrete factor colouring with a legend of group levels, optional density/statistical overlays, and group mark / label annotations.
features — continuous numeric colouring with a gradient colour bar, multi-feature faceting via tidyr::pivot_longer(), and optional cutoff / quantile trimming via prepare_continuous_color_scale().

Additional annotation layers include: graph / network edges drawn as segments between connected nodes, 2D density contours (filled or outline), group marks (hull, ellipse, rect, circle via ggforce), lineage curves (LOESS-smoothed paths with optional whiskers), velocity / RNA-velocity arrows (raw, grid, or stream via VelocityPlot()), statistical summary mini-plots (pie, ring, bar, line) embedded at group centroids, background points from other facets (faded context), and group labels with repulsion (via ggrepel::geom_text_repel()).

Rendering scales automatically: scatter points for small datasets, scattermore::geom_scattermore() raster for n > 1e5, or hex-binned aggregation (stat_summary_hex() / geom_hex()). Legend assembly uses cowplot::get_plot_component() with independent guide-boxes for base groups, lineages, velocity, and stat-by annotations — combined via rbind / cbind and re-inserted with add_grob().

Usage

DimPlotAtomic(
  data,
  dims = 1:2,
  group_by = NULL,
  group_by_sep = "_",
  features = NULL,
  lower_quantile = 0,
  upper_quantile = 0.99,
  lower_cutoff = NULL,
  upper_cutoff = NULL,
  pt_size = NULL,
  pt_alpha = 1,
  bg_color = "grey80",
  bg_cutoff = NULL,
  color_name = "",
  label_insitu = FALSE,
  show_stat = !identical(theme, "theme_blank"),
  label = FALSE,
  label_size = 4,
  label_fg = "white",
  label_bg = "black",
  label_bg_r = 0.1,
  label_repel = FALSE,
  label_repulsion = 20,
  label_pt_size = 1,
  label_pt_color = "black",
  label_segment_color = "black",
  order = c("as-is", "reverse", "high-top", "low-top", "random"),
  highlight = NULL,
  highlight_alpha = 1,
  highlight_size = 1,
  highlight_color = "black",
  highlight_stroke = 0.8,
  add_mark = FALSE,
  mark_type = c("hull", "ellipse", "rect", "circle"),
  mark_expand = unit(3, "mm"),
  mark_alpha = 0.1,
  mark_linetype = 1,
  stat_by = NULL,
  stat_plot_type = c("pie", "ring", "bar", "line"),
  stat_plot_size = 0.1,
  stat_palette = "Set1",
  stat_args = list(),
  graph = NULL,
  edge_size = c(0.05, 0.5),
  edge_alpha = 0.1,
  edge_color = "grey40",
  add_density = FALSE,
  density_color = "grey80",
  density_filled = FALSE,
  density_filled_palette = "Greys",
  density_filled_palcolor = NULL,
  lineages = NULL,
  lineages_trim = c(0.01, 0.99),
  lineages_span = 0.75,
  lineages_palette = "Dark2",
  lineages_palcolor = NULL,
  lineages_arrow = ggplot2::arrow(length = unit(0.1, "inches")),
  lineages_linewidth = 1,
  lineages_line_bg = "white",
  lineages_line_bg_stroke = 0.5,
  lineages_whiskers = FALSE,
  lineages_whiskers_linewidth = 0.5,
  lineages_whiskers_alpha = 0.5,
  velocity = NULL,
  velocity_plot_type = c("raw", "grid", "stream"),
  velocity_n_neighbors = NULL,
  velocity_density = 1,
  velocity_smooth = 0.5,
  velocity_scale = 1,
  velocity_min_mass = 1,
  velocity_cutoff_perc = 5,
  velocity_group_palette = "Set2",
  velocity_group_palcolor = NULL,
  arrow_angle = 20,
  arrow_color = "black",
  streamline_l = 5,
  streamline_minl = 1,
  streamline_res = 1,
  streamline_n = 15,
  arrow_alpha = 1,
  streamline_width = c(0, 0.8),
  streamline_alpha = 1,
  streamline_color = NULL,
  streamline_palette = "RdYlBu",
  streamline_palcolor = NULL,
  streamline_bg_color = "white",
  streamline_bg_stroke = 0.5,
  keep_na = FALSE,
  keep_empty = FALSE,
  facet_by = NULL,
  facet_scales = "fixed",
  facet_nrow = NULL,
  facet_ncol = NULL,
  facet_byrow = TRUE,
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  theme = "theme_this",
  theme_args = list(),
  aspect.ratio = 1,
  legend.position = "right",
  legend.direction = "vertical",
  raster = NULL,
  raster_dpi = c(512, 512),
  hex = FALSE,
  hex_linewidth = 0.5,
  hex_count = !is.null(group_by),
  hex_bins = 50,
  hex_binwidth = NULL,
  palette = ifelse(is.null(features), "Paired", "Spectral"),
  palcolor = NULL,
  palreverse = FALSE,
  seed = 8525,
  ...
)

Arguments

`data`	A data frame.
`dims`	A character vector of the column names to plot on the x, y (and optionally z) axes or a numeric vector of the column indices. When 3 dimensions are provided, a 3D interactive plot is created using plotly. Supported in 3D: group_by, features, labels, highlight, lineages, graph/network, show_stat, order. Not supported in 3D: add_mark, stat_by, add_density, velocity, hex, facet_by, raster.
`group_by`	A character string of the column name to group the data by for discrete colouring. A character/factor column is expected. If multiple columns are provided, the columns will be concatenated with `group_by_sep`.
`group_by_sep`	A character string to concatenate the columns in `group_by`, if multiple columns are provided.
`features`	A character vector of the column names to plot as features (continuous colouring). When multiple features are provided and `facet_by` is not set, the data is pivoted to long format and faceted by feature name.
`lower_quantile`, `upper_quantile`	Lower and upper quantiles for the continuous color/fill scale. The actual cutoffs are determined by these quantiles when `lower_cutoff` and `upper_cutoff` are `NULL`. Defaults: `lower_quantile = 0`, `upper_quantile = 0.99`.
`lower_cutoff`, `upper_cutoff`	Explicit lower and upper cutoffs for the continuous color/fill scale. When `NULL` (the default), the cutoffs are determined by `lower_quantile` and `upper_quantile` via `quantile`. Values outside the `[lower_cutoff, upper_cutoff]` range are clamped (winsorized) to the nearest cutoff value.
`pt_size`	A numeric value of the point size. If NULL (default), the point size is auto-calculated as `min(3000 / nrow(data), 0.6)` so large datasets automatically get smaller points.
`pt_alpha`	A numeric value in `⁠[0, 1]⁠` for the point transparency. Default is `1`.
`bg_color`	A character string specifying the colour used for NA-valued points and background context points drawn from other facets. Default is `"grey80"`.
`bg_cutoff`	A numeric threshold. Feature values with absolute value below this cutoff are set to `NA` (and therefore rendered in `bg_color`). Default is `NULL`.
`color_name`	A character string used as the title for the continuous colour bar in feature mode. Default is `""`.
`label_insitu`	A logical value. If `TRUE`, the raw group names are placed at the group median coordinates instead of numeric indices. Forces `label = TRUE`. Default is `FALSE`.
`show_stat`	A logical value. If `TRUE` (default), the number of points per group is shown in the legend labels and subtitle. Ignored when `theme = "theme_blank"`.
`label`	A logical value. If `TRUE`, group labels (numeric indices by default, or group names when `label_insitu = TRUE`) are placed at the median coordinates of each group. Forced to `TRUE` when `label_repel` or `label_insitu` is set.
`label_size`	A numeric value for the label text size. Passed to `ggrepel::geom_text_repel()`. Default is `4`.
`label_fg`	A character string for the label text (foreground) colour. Default is `"white"`.
`label_bg`	A character string for the label background / outline colour. Default is `"black"`.
`label_bg_r`	A numeric value for the background fill ratio of the label bounding box. Passed to `ggrepel::geom_text_repel(bg.r = ...)`. Default is `0.1`.
`label_repel`	A logical value. If `TRUE`, labels are repelled from each other with force `label_repulsion`. A visible point anchor is drawn. Forces `label = TRUE`.
`label_repulsion`	A numeric value for the repulsion force when `label_repel = TRUE`. Passed to `ggrepel::geom_text_repel(force = ...)`. Default is `20`.
`label_pt_size`	A numeric value for the size of the anchor point drawn when `label_repel = TRUE`. Default is `1`.
`label_pt_color`	A character string for the colour of the label anchor point. Default is `"black"`.
`label_segment_color`	A character string for the colour of the line segment connecting the label to the anchor. Used in non-repel mode (`label_repel = FALSE`) where `min.segment.length = 0`. Default is `"black"`.
`order`	A character string controlling the draw order of points: `"as-is"` (default) — the row order in the data is preserved. `"reverse"` — rows are reversed. `"high-top"` — points with high values (last factor levels for group_by) are drawn last (on top). `"low-top"` — points with low values (first factor levels) are drawn last. `"random"` — rows are randomly shuffled. For `high-top` and `low-top`, NA values are always plotted at the bottom. When applied to `group_by`, only the draw order changes — legend colours and order are unaffected. Within the same level, point order is preserved. For precise control, set factor levels before plotting. See https://github.com/pwwang/scplotter/issues/29#issuecomment-3009694130 for examples.
`highlight`	A specification for highlighted points: `NULL` (default): no highlighting. `TRUE`: highlight all points (adds a dark outline around every point). A character string: a dplyr filter expression (e.g., `"clusters == 'Ductal'"`). A character vector: row names to highlight. A numeric vector: row indices to highlight.
`highlight_alpha`	A numeric value in `⁠[0, 1]⁠` for the transparency of highlighted points. Default is `1`.
`highlight_size`	A numeric value for the size of the inner (coloured) highlight point. Default is `1`.
`highlight_color`	A character string for the colour of the outer highlight ring. Default is `"black"`.
`highlight_stroke`	A numeric value for the thickness of the outer highlight ring (the difference between the outer ring size and `highlight_size`). Default is `0.8`.
`add_mark`	A logical value. If `TRUE`, group boundaries are drawn around points using `ggforce` marks. Requires `group_by`. Only supported in 2D.
`mark_type`	A character string specifying the mark shape. Options: `"hull"` (convex hull, default), `"ellipse"`, `"rect"`, or `"circle"`.
`mark_expand`	A unit value for the outward expansion of the mark boundary. Passed to `ggforce::geom_mark_*(expand = ...)`. Default is `unit(3, "mm")`.
`mark_alpha`	A numeric value in `⁠[0, 1]⁠` for the transparency of the mark fill. Default is `0.1`.
`mark_linetype`	A numeric value for the line type of the mark boundary. Default is `1` (solid).
`stat_by`	A character string naming a column used to compute per-group statistical summary mini-plots embedded at group centroid positions. Only supported with `group_by` (not `features`). Only supported in 2D without `facet_by`.
`stat_plot_type`	A character string specifying the mini-plot type. Options: `"pie"` (default), `"ring"`, `"bar"`, or `"line"`.
`stat_plot_size`	A numeric value for the size of the stat mini-plot, expressed as a fraction of the axis range. Default is `0.1`.
`stat_args`	A list of additional arguments passed to the stat plot function (e.g., `list(palette = "Set1")`). Default is `list(palette = "Set1")`.
`graph`	A specification for network / graph edges to overlay. Sources: A character string starting with `"@"` (e.g., `"@graph"`): extracts the attribute named `"graph"` from `attributes(data)`. A `Graph` object (e.g., Seurat): coerced to dense matrix via `as.matrix()`. A `matrix`, `data.frame`, or `dgCMatrix`: used directly as the adjacency matrix. Numeric indices or character column names: extracts columns from `data`. Edges are drawn for non-zero, lower-triangle entries. Requires `data` to have row names matching the matrix dimnames.
`edge_size`	A numeric vector of length 2 specifying the range `⁠[min, max]⁠` for `scale_linewidth_continuous(range = ...)` applied to edge widths. Default is `c(0.05, 0.5)`.
`edge_alpha`	A numeric value in `⁠[0, 1]⁠` for the transparency of graph edges. Default is `0.1`.
`edge_color`	A character string for the colour of graph edges. Default is `"grey40"`.
`add_density`	A logical value. If `TRUE`, a 2D density layer is overlaid. Only supported in 2D.
`density_color`	A character string for the colour of the density contour lines. Used when `density_filled = FALSE`. Default is `"grey80"`.
`density_filled`	A logical value. If `TRUE`, the density is rendered as a filled raster (`stat_density_2d(geom = "raster")`) instead of contour lines. A separate fill scale is used.
`density_filled_palette`	A character string naming the palette for the filled density layer. Default is `"Greys"`.
`density_filled_palcolor`	A character vector of specific colours for the filled density palette. Default is `NULL` (auto-resolved from `density_filled_palette`).
`lineages`	A character vector of column names representing pseudotime / trajectory lineages. Each column is fitted with a LOESS smooth (`⁠span = lineages_span, degree = 2⁠`) across the 2D embedding, after trimming the top and bottom `lineages_trim` quantiles. Only supported in 2D without `facet_by`.
`lineages_trim`	A numeric vector of length 2 specifying the lower and upper quantile thresholds `⁠[0, 1]⁠` for trimming lineage values before LOESS fitting. Default is `c(0.01, 0.99)`.
`lineages_span`	A numeric value passed as `span` to `stats::loess()` controlling the smoothness of the lineage curve. Smaller values follow the data more closely. Default is `0.75`.
`lineages_palette`	A character string naming the palette for lineage colours. Default is `"Dark2"`.
`lineages_palcolor`	A character vector of specific colours for lineage curves. Default is `NULL` (auto-resolved from `lineages_palette`).
`lineages_arrow`	A ggplot2 `arrow` specification applied to the end of lineage paths. Default is `arrow(length = unit(0.1, "inches"))`.
`lineages_linewidth`	A numeric value for the width of the lineage curve lines. Default is `1`.
`lineages_line_bg`	A character string for the colour of the background (wider) stroke drawn behind each lineage curve for improved visibility. Default is `"white"`.
`lineages_line_bg_stroke`	A numeric value for the additional width of the background stroke relative to `lineages_linewidth`. The background line has total width `lineages_linewidth + lineages_line_bg_stroke`. Default is `0.5`.
`lineages_whiskers`	A logical value. If `TRUE`, short line segments connect the smoothed lineage curve to the original data coordinates of the fitted points. Default is `FALSE`.
`lineages_whiskers_linewidth`	A numeric value for the width of the whisker lines. Default is `0.5`.
`lineages_whiskers_alpha`	A numeric value in `⁠[0, 1]⁠` for the transparency of the whisker lines. Default is `0.5`.
`velocity`	A specification for RNA-velocity arrows. Can be: `NULL` (default): no velocity overlay. A character / integer vector: column names or indices in `data` for the velocity embedding. A data frame or matrix: the velocity embedding itself (must align with `data` rows). Only supported in 2D without `facet_by`.
`velocity_plot_type`	A character string specifying the velocity rendering style. Options: `"raw"` (arrows from embedding), `"grid"` (grid-based arrows), or `"stream"` (streamlines). Default is `"raw"`.
`velocity_n_neighbors`	A numeric value for the number of neighbours used in the velocity grid computation. Default is `NULL` (auto).
`velocity_density`	A numeric value for the velocity kernel density bandwidth. Default is `1`.
`velocity_smooth`	A numeric value for the velocity smoothing parameter. Default is `0.5`.
`velocity_scale`	A numeric value for scaling the velocity arrows. Default is `1`.
`velocity_min_mass`	A numeric value for the minimum cell mass threshold in velocity grid computation. Default is `1`.
`velocity_cutoff_perc`	A numeric value for the velocity cutoff percentage. Default is `5`.
`velocity_group_palette`	A character string naming the palette for velocity group colours (used in `"raw"` plot type). Default is `"Set2"`.
`velocity_group_palcolor`	A character vector of specific colours for velocity groups. Default is `NULL` (auto-resolved from `velocity_group_palette`).
`arrow_angle`	A numeric value specifying the angle of the arrowheads in degrees. Applied to `arrow` when `plot_type` is `"raw"` or `"grid"`. Default is 20.
`arrow_color`	A character string specifying the color of the velocity arrows. For `plot_type = "stream"`, this sets only the arrowhead color. Default is `"black"`.
`streamline_l`	A numeric value specifying the integration length of the streamlines. Passed to `geom_streamline` as the `L` parameter. Default is 5.
`streamline_minl`	A numeric value specifying the minimum streamline length. Shorter streamlines are not drawn. Passed to `geom_streamline` as the `min.L` parameter. Default is 1.
`streamline_res`	A numeric value specifying the resolution of the streamline integration. Passed to `geom_streamline` as the `res` parameter. Default is 1.
`streamline_n`	A numeric value specifying the number of streamlines to draw. Passed to `geom_streamline` as the `n` parameter. Default is 15.
`arrow_alpha`	A numeric value between 0 and 1 specifying the transparency of the velocity arrows. Only used when `plot_type = "raw"` or `"grid"`; for `plot_type = "stream"`, use `streamline_alpha` instead. Default is 1.
`streamline_width`	A numeric vector of length 2 specifying the range of line widths for streamlines. Passed to `scale_size(range = ...)`. Only used when `streamline_color` is `NULL`. Default is `c(0, 0.8)`.
`streamline_alpha`	A numeric value between 0 and 1 specifying the transparency of the velocity streamlines. Default is 1.
`streamline_color`	An optional character string specifying a fixed color for streamlines. When `NULL` (the default), streamlines are colored by velocity magnitude using `streamline_palette`.
`streamline_palette`	A character string specifying the color palette for streamline velocity magnitude. Passed to `palette_this`. Only used when `streamline_color` is `NULL`. Default is `"RdYlBu"`.
`streamline_palcolor`	An optional character vector of specific colors for the streamline velocity gradient. If `NULL`, colors are generated from `streamline_palette`. Default is `NULL`.
`streamline_bg_color`	A character string specifying the background (outline) color applied to streamlines to create a stroke effect. Default is `"white"`.
`streamline_bg_stroke`	A numeric value specifying the additional line width of the background stroke relative to the foreground streamline. Default is 0.5.
`keep_na`	A logical value or a character to replace the NA values in the data. It can also take a named list to specify different behavior for different columns. If TRUE or NA, NA values will be replaced with NA. If FALSE, NA values will be removed from the data before plotting. If a character string is provided, NA values will be replaced with the provided string. If a named vector/list is provided, the names should be the column names to apply the behavior to, and the values should be one of TRUE, FALSE, or a character string. Without a named vector/list, the behavior applies to categorical/character columns used on the plot, for example, the `x`, `group_by`, `fill_by`, etc.
`keep_empty`	One of FALSE, TRUE and "level". It can also take a named list to specify different behavior for different columns. Without a named list, the behavior applies to the categorical/character columns used on the plot, for example, the `x`, `group_by`, `fill_by`, etc. `FALSE` (default): Drop empty factor levels from the data before plotting. `TRUE`: Keep empty factor levels and show them as a separate category in the plot. `"level"`: Keep empty factor levels, but do not show them in the plot. But they will be assigned colors from the palette to maintain consistency across multiple plots. Alias: `levels`
`facet_by`	A character string specifying the column name of the data frame to facet the plot. Otherwise, the data will be split by `split_by` and generate multiple plots and combine them into one using `patchwork::wrap_plots`
`facet_scales`	Whether to scale the axes of facets. Default is "fixed" Other options are "free", "free_x", "free_y". See `ggplot2::facet_wrap`
`facet_nrow`	A numeric value specifying the number of rows in the facet. When facet_by is a single column and facet_wrap is used.
`facet_ncol`	A numeric value specifying the number of columns in the facet. When facet_by is a single column and facet_wrap is used.
`facet_byrow`	A logical value indicating whether to fill the plots by row. Default is TRUE.
`title`	A character string specifying the title of the plot. A function can be used to generate the title based on the default title. This is useful when split_by is used and the title needs to be dynamic.
`subtitle`	A character string specifying the subtitle of the plot.
`xlab`	A character string specifying the x-axis label.
`ylab`	A character string specifying the y-axis label.
`theme`	A character string or a theme class (i.e. ggplot2::theme_classic) specifying the theme to use. Default is "theme_this".
`theme_args`	A list of arguments to pass to the theme function.
`aspect.ratio`	A numeric value specifying the aspect ratio of the plot.
`legend.position`	A character string specifying the position of the legend. if `waiver()`, for single groups, the legend will be "none", otherwise "right".
`legend.direction`	A character string specifying the direction of the legend.
`raster`	A logical value. If `TRUE`, points are rendered via `scattermore::geom_scattermore()` for efficient rasterised plotting. Default is `NULL`, which auto-enables when `nrow(data) > 1e5`.
`raster_dpi`	A numeric vector of length 2 `⁠[x_dpi, y_dpi]⁠` specifying the raster resolution in pixels. Passed to `scattermore::geom_scattermore(pixels = ...)`. Default is `c(512, 512)`. If a single value is provided it is recycled to both dimensions.
`hex`	A logical value. If `TRUE`, points are rendered as hexagonal bins via `geom_hex()` / `stat_summary_hex()`. Not supported with highlight. Default is `FALSE`. Only supported in 2D.
`hex_linewidth`	A numeric value for the width of the hexagon boundary lines. Default is `0.5`.
`hex_count`	A logical value. If `TRUE` and `group_by` is set, hex fill alpha is mapped to `after_stat(count)` so denser bins are more opaque. For `features` mode hex_count is ignored. Default is `!is.null(group_by)`.
`hex_bins`	A numeric value for the number of hex bins along each axis. Passed to `geom_hex(bins = ...)`. Default is `50`.
`hex_binwidth`	A numeric value for the width of individual hex bins. Passed to `geom_hex(binwidth = ...)`. Takes precedence over `hex_bins` when set.
`palette`	A character string specifying the palette to use. A named list or vector can be used to specify the palettes for different `split_by` values.
`palcolor`	A character string specifying the color to use in the palette. A named list can be used to specify the colors for different `split_by` values. If some values are missing, the values from the palette will be used (palcolor will be NULL for those values).
`palreverse`	A logical value indicating whether to reverse the palette. Default is FALSE.
`seed`	The random seed to use. Default is 8525.
`...`	Additional arguments.

Value

A ggplot object or a plotly object (when 3 dimensions are provided)

Architecture

DimPlotAtomic executes the following steps:

ggplot dispatch — selects gglogger::ggplot or ggplot2::ggplot.
Order validation — match.arg(order).
Dimension resolution — converts numeric indices to column names, validates exactly 2 or 3 dims via check_columns().
Column resolution — validates group_by (force_factor, concat_multi), features, and facet_by. Requires at least one of group_by or features. Blocks facet_by when multiple features are present (features themselves become facets).
Auto defaults — pt_size defaults to min(3000 / nrow(data), 0.6); raster auto-enables when nrow(data) > 1e5; theme_blank suppresses axis labels.
Label force-enable — if label_repel or label_insitu is TRUE, label is forced to TRUE with a message.
NA / empty handling — process_keep_na_empty() filters the data; keep_empty values extracted for group_by and facet_by.
group_by preprocessing — group values / colours resolved via palette_this(). NA levels mapped to literal "NA" string. label_use is constructed based on label, label_insitu, and show_stat combinations. Facet labeller is set to as_labeller() with per-facet N annotations when show_stat = TRUE.
Multi-feature pivot — when length(features) > 1, data is pivoted to long format via tidyr::pivot_longer() with .feature as the facet variable and .value as the numeric column.
Continuous colour scale — when features is set, prepare_continuous_color_scale() applies quantile/cutoff trimming and returns anchor values for the gradient.
Point ordering — applies the selected order strategy (as-is, reverse, high-top, low-top, random) by sorting or shuffling rows.
3D branch — if length(dims) == 3, emits a warning for unsupported features, optionally down-samples with stratified group sampling (when raster = TRUE), and delegates to DimPlotAtomic3D().
Group marks (2D only, when add_mark = TRUE) — dispatches to ggforce::geom_mark_hull/ellipse/rect/circle, with new_scale_fill() / new_scale_color() to isolate mark scales.
Graph / network (2D only) — resolves the graph source (same logic as 3D), melts the matrix, handles faceted data by per-facet edge splitting, and adds geom_segment(aes(linewidth = value)) with scale_linewidth_continuous().
Density overlay (2D only) — filled (stat_density_2d(geom = "raster")) or outline (geom_density_2d()).
Base scales and theme — x / y limits from data range, do_call(theme, theme_args), aspect ratio and legend position.
Background points for facet context — for faceted plots (excluding multi-feature auto-faceting), points from other facets are added as faded background (raster / hex / point depending on settings).
Main point layer — dispatches by rendering mode:
- raster: scattermore::geom_scattermore() with separate NA / non-NA group layers.
- hex: geom_hex() (group_by with optional count alpha, or stat_summary_hex() for features). Raises has_fill = TRUE.
- standard: geom_point().
Highlight (2D only) — resolves highlight specification (TRUE, filter expression, row names, indices), errors on hex + highlight combo, renders highlight points with stroke (outer ring + inner colour).
Colour scales — scale_color_manual() for group_by (with keep_empty-aware breaks/limits/drop), or scale_color_gradientn() for features. scale_fill_manual() / scale_fill_gradientn() added when has_fill is TRUE.
Base legend — extracted via cowplot::get_plot_component("guide-box-bottom").
Lineages (2D only, no facet_by) — per-lineage LOESS fitting (⁠span = lineages_span, degree = 2⁠) with optional whiskers connecting smoothed to raw coordinates. Rendered as geom_path() with background stroke + foreground colour, plus scale_color_manual(). Legend extracted as a separate guide-box.
Velocity (2D only, no facet_by) — delegates to VelocityPlot() with return_layer = TRUE. Adds new_scale_color() when the velocity layer has its own colour scale. Legend extracted separately.
Stat-by mini-plots (2D only, no facet_by, no features) — dispatches to PieChart() / RingPlot() / BarPlot() / LinePlot() via do_call(). Each mini-plot is rendered as annotation_custom() at the group's median coordinates, scaled by stat_plot_size * range. Legend extracted from the stat plot.
Group labels (2D only, no features) — geom_text_repel() with optional repulsion (force = label_repulsion) or fixed segments (force = 0, bold, min.segment.length = 0). Labels positioned at group median coordinates (computed per facet if applicable).
Legend assembly — when additional legends exist (lineages, velocity, stat_by), they are combined with the base legend via cbind (vertical direction) or rbind (horizontal). The combined legend is re-inserted via add_grob(gtable, legend, legend.position).
Dimension calculation — calculate_plot_dimensions(base_height = 5.5, aspect.ratio, legend_n, legend_nchar) sets height / width attributes.
Faceting — facet_plot() is called only when no additional legends were assembled (otherwise the combined-legend grob is returned directly).