Statistic Plot

Visualizes data using various plot types such as bar plots, rose plots, ring plots, pie charts, trend plots, area plots, dot plots, sankey plots, chord plots, venn diagrams, and upset plots.

Usage

StatPlot(
  meta.data,
  stat.by,
  group.by = NULL,
  split.by = NULL,
  bg.by = 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", "area", "dot", "sankey", "chord",
    "venn", "upset"),
  stat_type = c("percent", "count"),
  position = c("stack", "dodge"),
  palette = "Paired",
  palcolor = NULL,
  alpha = 1,
  bg_palette = "Paired",
  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(),
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  force = FALSE,
  seed = 11
)

Arguments

meta.data: The data frame containing the data to be plotted.
stat.by: The column name(s) in meta.data specifying the variable(s) to be plotted.
group.by: Name of one or more meta.data columns to group (color) cells by.
split.by: Name of a column in meta.data column to split plot by. Default is NULL.
bg.by: The column name in meta.data specifying the background variable for bar plots.
flip: Whether to flip the plot. Default is FALSE.
NA_color: The color to use for missing values.
NA_stat: Whether to include missing values in the plot. Default is TRUE.
keep_empty: Whether to keep empty groups in the plot. Default is FALSE.
individual: Whether to plot individual groups separately. Default is FALSE.
stat_level: The level(s) of the variable(s) specified in stat.by to include in the plot. Default is NULL.
plot_type: The type of plot to create. Can be one of "bar", "rose", "ring", "pie", "trend", "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: Color palette name. Available palettes can be found in thisplot::show_palettes. Default is "Paired".
palcolor: Custom colors used to create a color palette. Default is NULL.
alpha: The transparency level for the plot.
bg_palette: The name of the background color palette to use for bar plots.
bg_palcolor: The color to use in the background color palette.
bg_alpha: The transparency level for the background color in bar plots.
label: Whether to add labels on the plot. Default is FALSE.
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: Aspect ratio of the panel. Default is NULL.
title: The text for the title. Default is NULL.
subtitle: The text for the subtitle for the plot which will be displayed below the title. Default is NULL.
xlab: The x-axis label of the plot. Default is NULL.
ylab: The y-axis label of the plot. Default is NULL.
legend.position: The position of legends, one of "none", "left", "right", "bottom", "top". Default is "right".
legend.direction: The direction of the legend in the plot. Can be one of "vertical" or "horizontal".
theme_use: Theme used. Can be a character string or a theme function. Default is "theme_scop".
theme_args: Other arguments passed to the theme_use. Default is list().
combine: Combine plots into a single patchwork object. If FALSE, return a list of ggplot objects.
nrow: Number of rows in the combined plot. Default is NULL, which means determined automatically based on the number of plots.
ncol: Number of columns in the combined plot. Default is NULL, which means determined automatically based on the number of plots.
byrow: Whether to arrange the plots by row in the combined plot. Default is TRUE.
force: Whether to force drawing regardless of maximum levels in any cell group is greater than 100. Default is FALSE.
seed: Random seed for reproducibility. Default is 11.

Examples

data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
#> ℹ [2026-01-22 04:23:44] Start standard scop workflow...
#> ℹ [2026-01-22 04:23:45] Checking a list of <Seurat>...
#> ! [2026-01-22 04:23:45] Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2026-01-22 04:23:45] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on the data 1/1 of the `srt_list`...
#> ℹ [2026-01-22 04:23:47] Perform `Seurat::FindVariableFeatures()` on the data 1/1 of the `srt_list`...
#> ℹ [2026-01-22 04:23:48] Use the separate HVF from srt_list
#> ℹ [2026-01-22 04:23:48] Number of available HVF: 2000
#> ℹ [2026-01-22 04:23:48] Finished check
#> ℹ [2026-01-22 04:23:48] Perform `Seurat::ScaleData()`
#> ℹ [2026-01-22 04:23:49] Perform pca linear dimension reduction
#> ℹ [2026-01-22 04:23:50] Perform `Seurat::FindClusters()` with `cluster_algorithm = 'louvain'` and `cluster_resolution = 0.6`
#> ℹ [2026-01-22 04:23:50] Reorder clusters...
#> ℹ [2026-01-22 04:23:50] Perform umap nonlinear dimension reduction
#> ℹ [2026-01-22 04:23:50] Non-linear dimensionality reduction (umap) using (Standardpca) dims (1-50) as input
#> ℹ [2026-01-22 04:23:55] Non-linear dimensionality reduction (umap) using (Standardpca) dims (1-50) as input
#> ✔ [2026-01-22 04:23:59] Run scop standard workflow completed
meta.data <- pancreas_sub@meta.data
StatPlot(
  meta.data,
  stat.by = "Phase",
  group.by = "CellType",
  plot_type = "bar",
  label = TRUE
)


StatPlot(
  GetFeaturesData(pancreas_sub, "RNA"),
  stat.by = "highly_variable_genes",
  plot_type = "ring",
  label = TRUE,
  NA_stat = FALSE
)


if (FALSE) { # \dontrun{
pancreas_sub <- AnnotateFeatures(
  pancreas_sub,
  species = "Mus_musculus",
  IDtype = "symbol",
  db = c("CSPA", "TF")
)
StatPlot(
  GetFeaturesData(pancreas_sub, "RNA"),
  stat.by = "TF",
  group.by = "CSPA",
  stat_type = "count",
  plot_type = "bar",
  position = "dodge",
  label = TRUE,
  NA_stat = FALSE
)
} # }

Usage

Arguments

See also

Examples