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Statistical plot of cells

Source: R/CellStatPlot.R
CellStatPlot.Rd

Statistical plot of cells

Usage

CellStatPlot(
  srt,
  stat.by,
  group.by = NULL,
  split.by = NULL,
  bg.by = NULL,
  cells = NULL,
  flip = FALSE,
  NA_color = "grey",
  NA_stat = TRUE,
  keep_empty = FALSE,
  individual = FALSE,
  stat_level = NULL,
  plot_type = c("bar", "rose", "ring", "pie", "trend", "trend_alluvial", "area", "dot",
    "sankey", "chord", "venn", "upset"),
  stat_type = c("percent", "count"),
  position = c("stack", "dodge"),
  palette = "Chinese",
  palcolor = NULL,
  alpha = 1,
  bg_palette = "Chinese",
  bg_palcolor = NULL,
  bg_alpha = 0.2,
  label = FALSE,
  label.size = 3.5,
  label.fg = "black",
  label.bg = "white",
  label.bg.r = 0.1,
  aspect.ratio = NULL,
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  theme_use = "theme_scop",
  theme_args = list(),
  x_text_angle = 45,
  grid_major = TRUE,
  grid_major_colour = "grey80",
  grid_major_linetype = 2,
  grid_major_linewidth = 0.3,
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  force = FALSE,
  seed = 11,
  ...
)

Arguments

srt

A Seurat object.

stat.by

Features to plot.

group.by

Metadata column(s) used to color cells.

split.by

Metadata column to facet by.

bg.by

Metadata column used as background color.

cells

Cell names to include.

flip

Flip x and y.

NA_color

The color to use for missing values.

NA_stat

Whether to include missing values in the plot.

keep_empty

Keep empty factor levels.

individual

One plot per group.

stat_level

The level(s) of the variable(s) specified in stat.by to include in the plot.

plot_type

The type of plot to create. Can be one of "bar", "rose", "ring", "pie", "trend", "trend_alluvial", "area", "dot", "sankey", "chord", "venn", or "upset".

stat_type

The type of statistic to compute for the plot. Can be one of "percent" or "count".

position

The position adjustment for the plot. Can be one of "stack" or "dodge".

palette, palcolor

Palette name (thisplot::show_palettes) or custom colors.

alpha

Plot transparency.

bg_palette, bg_palcolor, bg_alpha

Background palette and transparency.

label

Whether to add labels on the plot.

label.size

The size of the labels.

label.fg

The foreground color of the labels.

label.bg

The background color of the labels.

label.bg.r

The radius of the rounded corners of the label background.

aspect.ratio

Panel aspect ratio.

title

Plot title. NULL hides the title for merged/single panels. When multiple lineages are plotted and title is NULL, each panel is titled with its lineage column.

subtitle

Plot subtitle.

xlab

Plot labels.

ylab

Y-axis label.

legend.position

Legend placement ("none", "left", "right", "bottom", "top"), direction, and title. legend.title = NULL uses the group name.

legend.direction

Legend direction: "horizontal" or "vertical".

theme_use, theme_args

Theme name or function, plus extra theme arguments.

x_text_angle

Rotation angle for x-axis labels.

grid_major

Whether to show major panel grid lines.

grid_major_colour

Color of major panel grid lines.

grid_major_linetype

Linetype of major panel grid lines.

grid_major_linewidth

Line width of major panel grid lines.

combine, nrow, ncol, byrow

Combine plots with patchwork. combine = FALSE returns a list of ggplots.

force

Draw even when a grouping has more than 100 levels.

seed

Random seed.

...

Additional arguments passed to the plotting helpers.

See also

FeatureStatPlot

Examples

data(pancreas_sub)
pancreas_sub <- RunStandardWorkflow(pancreas_sub)
#> ℹ [2026-08-30 04:07:44] Start standard processing workflow...
#> ℹ [2026-08-30 04:07:44] Checking a list of <Seurat>...
#> ! [2026-08-30 04:07:44] Data 1/1 of the `srt_list` is "unknown"
#> Warning: Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2026-08-30 04:07:44] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on 1/1 of `srt_list`...
#> ℹ [2026-08-30 04:07:44] Perform `FindVariableFeatures()` on 1/1 of `srt_list`...
#> ℹ [2026-08-30 04:07:45] Use the separate HVF from `srt_list`
#> ℹ [2026-08-30 04:07:45] Number of available HVF: 2000
#> ℹ [2026-08-30 04:07:45] Finished check
#> ℹ [2026-08-30 04:07:45] Perform `ScaleData()`
#> ℹ [2026-08-30 04:07:45] Perform pca linear dimension reduction
#> ℹ [2026-08-30 04:07:45] Use stored estimated dimensions 1:23 for Standardpca
#> ℹ [2026-08-30 04:07:45] Perform `Seurat::FindClusters()` with `cluster_algorithm = 'louvain'` and `cluster_resolution = 0.6`
#> ℹ [2026-08-30 04:07:45] Reorder clusters...
#> ℹ [2026-08-30 04:07:45] Skip `log1p()` because `layer = data` is not "counts"
#> ℹ [2026-08-30 04:07:45] Perform umap nonlinear dimension reduction
#> ✔ [2026-08-30 04:07:52] Standard processing workflow completed
p1 <- CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "SubCellType",
  label = TRUE
)
p1


thisplot::panel_fix(
  p1,
  height = 2, width = 3
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "SubCellType",
  stat_type = "count",
  position = "dodge",
  label = TRUE
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "SubCellType",
  bg.by = "CellType",
  palette = "Set1",
  stat_type = "count",
  position = "dodge"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  plot_type = "bar"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  plot_type = "rose"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  plot_type = "ring"
)
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_col()`).


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  plot_type = "pie"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  plot_type = "dot"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  plot_type = "bar"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  plot_type = "rose"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  plot_type = "ring"
)
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_col()`).


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  plot_type = "area"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  plot_type = "dot"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  plot_type = "trend"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  plot_type = "trend_alluvial"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  plot_type = "bar",
  individual = TRUE
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  stat_type = "count",
  plot_type = "bar"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  stat_type = "count",
  plot_type = "rose"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  stat_type = "count",
  plot_type = "ring"
)
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_col()`).


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  stat_type = "count",
  plot_type = "area"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  stat_type = "count",
  plot_type = "dot"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  stat_type = "count",
  plot_type = "trend"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  stat_type = "count",
  plot_type = "bar",
  position = "dodge",
  label = TRUE
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  stat_type = "count",
  plot_type = "rose",
  position = "dodge",
  label = TRUE
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  stat_type = "count",
  plot_type = "ring",
  position = "dodge",
  label = TRUE
)
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_col()`).


CellStatPlot(
  pancreas_sub,
  stat.by = c("CellType", "Phase"),
  plot_type = "sankey"
)
#> ! [2026-08-30 04:08:02] `stat_type` is forcibly set to "count" when plot "sankey", "chord", "venn", and "upset"
#> Warning: `stat_type` is forcibly set to "count" when plot "sankey", "chord", "venn", and "upset"


CellStatPlot(
  pancreas_sub,
  stat.by = c("CellType", "Phase"),
  plot_type = "chord"
)
#> ! [2026-08-30 04:08:03] `stat_type` is forcibly set to "count" when plot "sankey", "chord", "venn", and "upset"
#> Warning: `stat_type` is forcibly set to "count" when plot "sankey", "chord", "venn", and "upset"


  CellStatPlot(
    pancreas_sub,
    stat.by = c("CellType", "Phase"),
    plot_type = "venn",
    stat_level = list(
      CellType = c("Ductal", "Ngn3-low-EP"),
      Phase = "S"
    )
  )
#> ! [2026-08-30 04:08:03] `stat_type` is forcibly set to "count" when plot "sankey", "chord", "venn", and "upset"
#> Warning: `stat_type` is forcibly set to "count" when plot "sankey", "chord", "venn", and "upset"


pancreas_sub$Progenitor <- pancreas_sub$CellType %in% c("Ngn3-low-EP", "Ngn3-high-EP")
pancreas_sub$G2M <- pancreas_sub$Phase == "G2M"
pancreas_sub$Fancb_Expressed <- GetAssayData5(
  pancreas_sub,
  assay = "RNA",
  layer = "counts"
)["Fancb", ] > 0
pancreas_sub$Dlg3_Expressed <- GetAssayData5(
  pancreas_sub,
  assay = "RNA",
  layer = "counts"
)["Dlg3", ] > 0

CellStatPlot(
  pancreas_sub,
  stat.by = c(
    "Progenitor", "G2M", "Fancb_Expressed", "Dlg3_Expressed"
  ),
  plot_type = "venn",
  stat_level = "TRUE"
)
#> ! [2026-08-30 04:08:03] `stat_type` is forcibly set to "count" when plot "sankey", "chord", "venn", and "upset"
#> Warning: `stat_type` is forcibly set to "count" when plot "sankey", "chord", "venn", and "upset"


CellStatPlot(
  pancreas_sub,
  stat.by = c(
    "Progenitor", "G2M", "Fancb_Expressed", "Dlg3_Expressed"
  ),
  plot_type = "upset",
  stat_level = "TRUE"
)
#> ! [2026-08-30 04:08:04] `stat_type` is forcibly set to "count" when plot "sankey", "chord", "venn", and "upset"
#> Warning: `stat_type` is forcibly set to "count" when plot "sankey", "chord", "venn", and "upset"
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the ggupset package.
#>   Please report the issue at <https://github.com/const-ae/ggupset/issues>.


sum(
  pancreas_sub$Progenitor == "FALSE" &
    pancreas_sub$G2M == "FALSE" &
    pancreas_sub$Fancb_Expressed == "TRUE" &
    pancreas_sub$Dlg3_Expressed == "FALSE"
)
#> [1] 6