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Feature statistical plots

Source: R/FeatureStatPlot.R
FeatureStatPlot.Rd

Feature statistical plots

Usage

FeatureStatPlot(
  srt,
  stat.by,
  group.by = NULL,
  split.by = NULL,
  bg.by = NULL,
  plot.by = c("group", "feature"),
  fill.by = c("group", "feature", "expression"),
  cells = NULL,
  layer = "data",
  assay = NULL,
  keep_empty = FALSE,
  individual = FALSE,
  plot_type = c("violin", "box", "bar", "dot", "col"),
  palette = "Chinese",
  palcolor = NULL,
  alpha = 1,
  bg_palette = "Chinese",
  bg_palcolor = NULL,
  bg_alpha = 0.2,
  add_box = FALSE,
  box_color = "black",
  box_width = 0.1,
  box_ptsize = 2,
  add_point = FALSE,
  pt.color = "grey30",
  pt.size = NULL,
  pt.alpha = 1,
  jitter.width = 0.4,
  jitter.height = 0.1,
  add_trend = FALSE,
  trend_color = "black",
  trend_linewidth = 1,
  trend_ptsize = 2,
  add_stat = c("none", "mean", "median"),
  stat_color = "black",
  stat_size = 1,
  stat_stroke = 1,
  stat_shape = 25,
  add_line = NULL,
  line_color = "red",
  line_size = 1,
  line_type = 1,
  cells.highlight = NULL,
  cols.highlight = "red",
  sizes.highlight = 1,
  alpha.highlight = 1,
  calculate_coexp = FALSE,
  same.y.lims = FALSE,
  y.min = NULL,
  y.max = NULL,
  y.trans = "identity",
  y.nbreaks = 5,
  sort = FALSE,
  stack = FALSE,
  flip = FALSE,
  comparisons = NULL,
  ref_group = NULL,
  auto_comparison = FALSE,
  pairwise_method = "wilcox.test",
  multiplegroup_comparisons = FALSE,
  multiple_method = "kruskal.test",
  sig_label = c("p.signif", "p.format"),
  sig_labelsize = 3.5,
  aspect.ratio = NULL,
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = "Expression level",
  legend.position = "right",
  legend.direction = "vertical",
  legend.title = NULL,
  theme_use = "theme_scop",
  theme_args = list(),
  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,
  ...,
  x_text_angle = 45,
  verbose = TRUE
)

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.

plot.by

"group" or "feature".

fill.by

"group", "feature", or "expression".

cells

Cell names to include.

layer

Assay layer to use.

assay

Assay to use. NULL uses the default assay.

keep_empty

Keep empty factor levels.

individual

One plot per group.

plot_type

"violin", "box", "bar", "dot", or "col".

palette, palcolor

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

alpha

Plot transparency.

bg_palette, bg_palcolor, bg_alpha

Background palette and transparency.

add_box, box_color, box_width, box_ptsize

Overlay boxplot.

add_point, pt.color, jitter.width, jitter.height

Overlay jittered points.

pt.size, pt.alpha

Point size and transparency. pt.size = NULL scales with sqrt(n) (minimum 0.3). Rasterized points keep at least a two-pixel radius at raster.dpi = c(512, 512) and scale with raster.dpi.

add_trend, trend_color, trend_linewidth, trend_ptsize

Overlay trend line.

add_stat, stat_color, stat_size, stat_stroke, stat_shape

Summary statistic ("none", "mean", or "median").

add_line, line_color, line_size, line_type

Horizontal line at this y-intercept.

cells.highlight

Cells to highlight and their appearance. TRUE highlights all cells.

cols.highlight, sizes.highlight, alpha.highlight

Highlighted cells.

calculate_coexp

Plot the geometric mean of stat.by.

same.y.lims

Share y-axis limits across panels.

y.min, y.max

Y-axis limits. Character values like "q5" use that quantile.

y.trans, y.nbreaks

Y-axis transform ("identity" or "log2") and breaks.

sort

Sort groups on the x-axis: FALSE, TRUE/"increasing", or "decreasing".

stack

Stack plots vertically.

flip

Flip x and y.

comparisons, ref_group

Pairwise comparisons (length-2 name or index vectors).

auto_comparison

Compare the highest-median group (or ref_group) against the others. Requires split.by = NULL.

pairwise_method, multiplegroup_comparisons, multiple_method

Comparison tests.

sig_label, sig_labelsize

Significance labels ("p.signif" or "p.format").

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.direction, legend.title

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

theme_use, theme_args

Theme name or function, plus extra theme arguments.

grid_major, grid_major_colour, grid_major_linetype, grid_major_linewidth

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.

x_text_angle

Rotation of x-axis labels.

verbose

Whether to print messages.

See also

CellStatPlot

Examples

data(pancreas_sub)
pancreas_sub <- RunStandardWorkflow(pancreas_sub)
#> ℹ [2026-08-30 04:29:45] Start standard processing workflow...
#> ℹ [2026-08-30 04:29:45] Checking a list of <Seurat>...
#> ! [2026-08-30 04:29:45] Data 1/1 of the `srt_list` is "unknown"
#> Warning: Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2026-08-30 04:29:45] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on 1/1 of `srt_list`...
#> ℹ [2026-08-30 04:29:45] Perform `FindVariableFeatures()` on 1/1 of `srt_list`...
#> ℹ [2026-08-30 04:29:45] Use the separate HVF from `srt_list`
#> ℹ [2026-08-30 04:29:45] Number of available HVF: 2000
#> ℹ [2026-08-30 04:29:46] Finished check
#> ℹ [2026-08-30 04:29:46] Perform `ScaleData()`
#> ℹ [2026-08-30 04:29:46] Perform pca linear dimension reduction
#> ℹ [2026-08-30 04:29:46] Use stored estimated dimensions 1:23 for Standardpca
#> ℹ [2026-08-30 04:29:46] Perform `Seurat::FindClusters()` with `cluster_algorithm = 'louvain'` and `cluster_resolution = 0.6`
#> ℹ [2026-08-30 04:29:46] Reorder clusters...
#> ℹ [2026-08-30 04:29:46] Skip `log1p()` because `layer = data` is not "counts"
#> ℹ [2026-08-30 04:29:46] Perform umap nonlinear dimension reduction
#> ✔ [2026-08-30 04:29:53] Standard processing workflow completed
FeatureStatPlot(
  pancreas_sub,
  stat.by = c("G2M_score", "Fev"),
  group.by = "SubCellType"
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.


FeatureStatPlot(
  pancreas_sub,
  stat.by = c("G2M_score", "Fev"),
  group.by = "SubCellType"
) |> thisplot::panel_fix(height = 1, width = 2)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.


FeatureStatPlot(
  pancreas_sub,
  stat.by = c("G2M_score", "Fev"),
  group.by = "SubCellType",
  plot_type = "box"
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.


FeatureStatPlot(
  pancreas_sub,
  stat.by = c("G2M_score", "Fev"),
  group.by = "SubCellType",
  plot_type = "bar"
)
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.


FeatureStatPlot(
  pancreas_sub,
  stat.by = c("G2M_score", "Fev"),
  group.by = "SubCellType",
  plot_type = "dot"
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.

FeatureStatPlot(
  pancreas_sub,
  stat.by = c("G2M_score", "Fev"),
  group.by = "SubCellType",
  plot_type = "col"
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.


FeatureStatPlot(
  pancreas_sub,
  stat.by = c("G2M_score", "Fev"),
  group.by = "SubCellType",
  add_box = TRUE
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.


FeatureStatPlot(
  pancreas_sub,
  stat.by = c("G2M_score", "Fev"),
  group.by = "SubCellType",
  add_point = TRUE
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.

FeatureStatPlot(
  pancreas_sub,
  stat.by = c("G2M_score", "Fev"),
  group.by = "SubCellType",
  add_trend = TRUE
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.


FeatureStatPlot(
  pancreas_sub,
  stat.by = c("G2M_score", "Fev"),
  group.by = "SubCellType",
  add_stat = "mean"
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.


FeatureStatPlot(
  pancreas_sub,
  stat.by = c("G2M_score", "Fev"),
  group.by = "SubCellType",
  add_line = 0.2,
  line_type = 2
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.


FeatureStatPlot(
  pancreas_sub,
  stat.by = c("G2M_score", "Fev"),
  group.by = "SubCellType",
  split.by = "Phase"
)
#> ! [2026-08-30 04:30:00] Removed 10 groups with < 2 observations for violin plot: "sp-S-gp-Beta", "sp-G2M-gp-Beta", "sp-S-gp-Pre-endocrine", "sp-G2M-gp-Pre-endocrine", "sp-S-gp-Alpha", "sp-G2M-gp-Alpha", "sp-S-gp-Epsilon", "sp-G2M-gp-Epsilon", "sp-S-gp-Delta", and "sp-G2M-gp-Delta"
#> Warning: Removed 10 groups with < 2 observations for violin plot: "sp-S-gp-Beta", "sp-G2M-gp-Beta", "sp-S-gp-Pre-endocrine", "sp-G2M-gp-Pre-endocrine", "sp-S-gp-Alpha", "sp-G2M-gp-Alpha", "sp-S-gp-Epsilon", "sp-G2M-gp-Epsilon", "sp-S-gp-Delta", and "sp-G2M-gp-Delta"
#> ! [2026-08-30 04:30:01] Removed 10 groups with < 2 observations for violin plot: "sp-S-gp-Beta", "sp-G2M-gp-Beta", "sp-S-gp-Pre-endocrine", "sp-G2M-gp-Pre-endocrine", "sp-S-gp-Alpha", "sp-G2M-gp-Alpha", "sp-S-gp-Epsilon", "sp-G2M-gp-Epsilon", "sp-S-gp-Delta", and "sp-G2M-gp-Delta"
#> Warning: Removed 10 groups with < 2 observations for violin plot: "sp-S-gp-Beta", "sp-G2M-gp-Beta", "sp-S-gp-Pre-endocrine", "sp-G2M-gp-Pre-endocrine", "sp-S-gp-Alpha", "sp-G2M-gp-Alpha", "sp-S-gp-Epsilon", "sp-G2M-gp-Epsilon", "sp-S-gp-Delta", and "sp-G2M-gp-Delta"
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.


FeatureStatPlot(
  pancreas_sub,
  stat.by = c("G2M_score", "Fev"),
  group.by = "SubCellType",
  split.by = "Phase",
  add_box = TRUE,
  add_trend = TRUE
)
#> ! [2026-08-30 04:30:01] Removed 10 groups with < 2 observations for violin plot: "sp-S-gp-Beta", "sp-G2M-gp-Beta", "sp-S-gp-Pre-endocrine", "sp-G2M-gp-Pre-endocrine", "sp-S-gp-Alpha", "sp-G2M-gp-Alpha", "sp-S-gp-Epsilon", "sp-G2M-gp-Epsilon", "sp-S-gp-Delta", and "sp-G2M-gp-Delta"
#> Warning: Removed 10 groups with < 2 observations for violin plot: "sp-S-gp-Beta", "sp-G2M-gp-Beta", "sp-S-gp-Pre-endocrine", "sp-G2M-gp-Pre-endocrine", "sp-S-gp-Alpha", "sp-G2M-gp-Alpha", "sp-S-gp-Epsilon", "sp-G2M-gp-Epsilon", "sp-S-gp-Delta", and "sp-G2M-gp-Delta"
#> ! [2026-08-30 04:30:01] Removed 10 groups with < 2 observations for violin plot: "sp-S-gp-Beta", "sp-G2M-gp-Beta", "sp-S-gp-Pre-endocrine", "sp-G2M-gp-Pre-endocrine", "sp-S-gp-Alpha", "sp-G2M-gp-Alpha", "sp-S-gp-Epsilon", "sp-G2M-gp-Epsilon", "sp-S-gp-Delta", and "sp-G2M-gp-Delta"
#> Warning: Removed 10 groups with < 2 observations for violin plot: "sp-S-gp-Beta", "sp-G2M-gp-Beta", "sp-S-gp-Pre-endocrine", "sp-G2M-gp-Pre-endocrine", "sp-S-gp-Alpha", "sp-G2M-gp-Alpha", "sp-S-gp-Epsilon", "sp-G2M-gp-Epsilon", "sp-S-gp-Delta", and "sp-G2M-gp-Delta"
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.


FeatureStatPlot(
  pancreas_sub,
  stat.by = c("G2M_score", "Fev"),
  group.by = "SubCellType",
  split.by = "Phase",
  comparisons = TRUE
)
#> ! [2026-08-30 04:30:03] Removed 10 groups with < 2 observations for violin plot: "sp-S-gp-Beta", "sp-G2M-gp-Beta", "sp-S-gp-Pre-endocrine", "sp-G2M-gp-Pre-endocrine", "sp-S-gp-Alpha", "sp-G2M-gp-Alpha", "sp-S-gp-Epsilon", "sp-G2M-gp-Epsilon", "sp-S-gp-Delta", and "sp-G2M-gp-Delta"
#> Warning: Removed 10 groups with < 2 observations for violin plot: "sp-S-gp-Beta", "sp-G2M-gp-Beta", "sp-S-gp-Pre-endocrine", "sp-G2M-gp-Pre-endocrine", "sp-S-gp-Alpha", "sp-G2M-gp-Alpha", "sp-S-gp-Epsilon", "sp-G2M-gp-Epsilon", "sp-S-gp-Delta", and "sp-G2M-gp-Delta"
#> ℹ [2026-08-30 04:30:03] Detected more than 2 groups. Use "kruskal.test" for comparison
#> ! [2026-08-30 04:30:03] Removed 10 groups with < 2 observations for violin plot: "sp-S-gp-Beta", "sp-G2M-gp-Beta", "sp-S-gp-Pre-endocrine", "sp-G2M-gp-Pre-endocrine", "sp-S-gp-Alpha", "sp-G2M-gp-Alpha", "sp-S-gp-Epsilon", "sp-G2M-gp-Epsilon", "sp-S-gp-Delta", and "sp-G2M-gp-Delta"
#> Warning: Removed 10 groups with < 2 observations for violin plot: "sp-S-gp-Beta", "sp-G2M-gp-Beta", "sp-S-gp-Pre-endocrine", "sp-G2M-gp-Pre-endocrine", "sp-S-gp-Alpha", "sp-G2M-gp-Alpha", "sp-S-gp-Epsilon", "sp-G2M-gp-Epsilon", "sp-S-gp-Delta", and "sp-G2M-gp-Delta"
#> ℹ [2026-08-30 04:30:03] Detected more than 2 groups. Use "kruskal.test" for comparison
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.


FeatureStatPlot(
  pancreas_sub,
  stat.by = c("Rbp4", "Pyy"),
  group.by = "SubCellType",
  fill.by = "expression",
  palette = "Blues",
  same.y.lims = TRUE
)


FeatureStatPlot(
  pancreas_sub,
  stat.by = c("Rbp4", "Pyy"),
  group.by = "SubCellType",
  multiplegroup_comparisons = TRUE
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.


FeatureStatPlot(
  pancreas_sub,
  stat.by = c("Rbp4", "Pyy"),
  group.by = "SubCellType",
  auto_comparison = TRUE,
  sig_label = "p.signif"
)
#> `stat_compare_means()` with `comparisons` displays *unadjusted* p-values (no correction for multiple comparisons).
#> ℹ For p-values adjusted for multiple comparisons, use `geom_pwc()`, or `stat_pvalue_manual()` together with `compare_means(..., p.adjust.method = )`.
#> This message is displayed once per session.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.


FeatureStatPlot(
  pancreas_sub,
  stat.by = c("Rbp4", "Pyy"),
  group.by = "SubCellType",
  comparisons = list(c("Alpha", "Beta"), c("Alpha", "Delta"))
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.


FeatureStatPlot(
  pancreas_sub,
  stat.by = c("Rbp4", "Pyy"),
  group.by = "SubCellType",
  comparisons = list(c("Alpha", "Beta"), c("Alpha", "Delta")),
  sig_label = "p.format"
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.


FeatureStatPlot(
  pancreas_sub,
  stat.by = "Fev",
  group.by = "SubCellType",
  split.by = "Phase",
  comparisons = TRUE
) + FeatureStatPlot(
  pancreas_sub,
  stat.by = "Fev",
  group.by = "SubCellType",
  split.by = "Phase",
  comparisons = TRUE,
  y.max = 5
)
#> ! [2026-08-30 04:30:09] Removed 10 groups with < 2 observations for violin plot: "sp-S-gp-Beta", "sp-G2M-gp-Beta", "sp-S-gp-Pre-endocrine", "sp-G2M-gp-Pre-endocrine", "sp-S-gp-Alpha", "sp-G2M-gp-Alpha", "sp-S-gp-Epsilon", "sp-G2M-gp-Epsilon", "sp-S-gp-Delta", and "sp-G2M-gp-Delta"
#> Warning: Removed 10 groups with < 2 observations for violin plot: "sp-S-gp-Beta", "sp-G2M-gp-Beta", "sp-S-gp-Pre-endocrine", "sp-G2M-gp-Pre-endocrine", "sp-S-gp-Alpha", "sp-G2M-gp-Alpha", "sp-S-gp-Epsilon", "sp-G2M-gp-Epsilon", "sp-S-gp-Delta", and "sp-G2M-gp-Delta"
#> ℹ [2026-08-30 04:30:09] Detected more than 2 groups. Use "kruskal.test" for comparison
#> ! [2026-08-30 04:30:09] Removed 10 groups with < 2 observations for violin plot: "sp-S-gp-Beta", "sp-G2M-gp-Beta", "sp-S-gp-Pre-endocrine", "sp-G2M-gp-Pre-endocrine", "sp-S-gp-Alpha", "sp-G2M-gp-Alpha", "sp-S-gp-Epsilon", "sp-G2M-gp-Epsilon", "sp-S-gp-Delta", and "sp-G2M-gp-Delta"
#> Warning: Removed 10 groups with < 2 observations for violin plot: "sp-S-gp-Beta", "sp-G2M-gp-Beta", "sp-S-gp-Pre-endocrine", "sp-G2M-gp-Pre-endocrine", "sp-S-gp-Alpha", "sp-G2M-gp-Alpha", "sp-S-gp-Epsilon", "sp-G2M-gp-Epsilon", "sp-S-gp-Delta", and "sp-G2M-gp-Delta"
#> ℹ [2026-08-30 04:30:09] Detected more than 2 groups. Use "kruskal.test" for comparison
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.


FeatureStatPlot(
  pancreas_sub,
  stat.by = c("Rbp4", "Pyy"),
  group.by = "SubCellType",
  bg.by = "CellType",
  add_box = TRUE, stack = TRUE
)


FeatureStatPlot(
  pancreas_sub,
  stat.by = c(
    # Ductal
    "Sox9", "Anxa2", "Bicc1",
    # EPs
    "Neurog3", "Hes6",
    # Pre-endocrine
    "Fev", "Neurod1",
    # Endocrine
    "Rbp4", "Pyy",
    # Beta, Alpha, Delta, Epsilon
    "Ins1", "Gcg", "Sst", "Ghrl"
  ),
  legend.position = "top",
  legend.direction = "horizontal",
  group.by = "SubCellType",
  bg.by = "CellType",
  stack = TRUE
)


FeatureStatPlot(
  pancreas_sub,
  stat.by = c(
    # Ductal
    "Sox9", "Anxa2", "Bicc1",
    # EPs
    "Neurog3", "Hes6",
    # Pre-endocrine
    "Fev", "Neurod1",
    # Endocrine
    "Rbp4", "Pyy",
    # Beta, Alpha, Delta, Epsilon
    "Ins1", "Gcg", "Sst", "Ghrl"
  ),
  fill.by = "feature",
  plot_type = "box",
  group.by = "SubCellType",
  bg.by = "CellType", stack = TRUE, flip = TRUE
) |> thisplot::panel_fix_overall(
  width = 8, height = 5
)


FeatureStatPlot(
  pancreas_sub,
  stat.by = c("Neurog3", "Rbp4", "Ins1"),
  group.by = "CellType",
  plot.by = "group"
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.


FeatureStatPlot(
  pancreas_sub,
  stat.by = c("Neurog3", "Rbp4", "Ins1"),
  group.by = "CellType",
  plot.by = "feature"
)
#> ℹ [2026-08-30 04:30:19] Setting `group.by` to "Features" as `plot.by` is set to "feature"
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.


FeatureStatPlot(
  pancreas_sub,
  stat.by = c("Neurog3", "Rbp4", "Ins1"),
  group.by = "CellType",
  plot.by = "feature",
  multiplegroup_comparisons = TRUE,
  sig_label = "p.format",
  sig_labelsize = 4
)
#> ℹ [2026-08-30 04:30:20] Setting `group.by` to "Features" as `plot.by` is set to "feature"
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.


FeatureStatPlot(
  pancreas_sub,
  stat.by = c("Neurog3", "Rbp4", "Ins1"),
  group.by = "CellType",
  plot.by = "feature",
  comparisons = list(
    c("Neurog3", "Rbp4"),
    c("Rbp4", "Ins1")
  ),
  stack = TRUE
)
#> ℹ [2026-08-30 04:30:23] Setting `group.by` to "Features" as `plot.by` is set to "feature"


FeatureStatPlot(pancreas_sub,
  stat.by = c(
    # Ductal
    "Sox9", "Anxa2", "Bicc1",
    # EPs
    "Neurog3", "Hes6",
    # Pre-endocrine
    "Fev", "Neurod1",
    # Endocrine
    "Rbp4", "Pyy",
    # Beta, Alpha, Delta, Epsilon
    "Ins1", "Gcg", "Sst", "Ghrl"
  ),
  group.by = "SubCellType",
  plot.by = "feature",
  stack = TRUE
)
#> ℹ [2026-08-30 04:30:25] Setting `group.by` to "Features" as `plot.by` is set to "feature"


data <- GetAssayData5(
  pancreas_sub,
  assay = "RNA",
  layer = "data"
)
pancreas_sub <- SeuratObject::SetAssayData(
  object = pancreas_sub,
  layer = "scale.data",
  assay = "RNA",
  new.data = data / Matrix::rowMeans(data)
)
#> Warning: Different features in new layer data than already exists for scale.data
FeatureStatPlot(
  pancreas_sub,
  stat.by = c("Neurog3", "Rbp4"),
  group.by = "CellType",
  layer = "scale.data",
  ylab = "FoldChange",
  same.y.lims = TRUE,
  y.max = 4
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.