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Visualization of Cell Screening Fractions

Source: R/30-ScreenFractionPlot.R
ScreenFractionPlot.Rd

Generates stacked bar plots showing the proportion of cells classified as Positive/Negative/Neutral by single-cell screening algorithms (Scissor, scPAS, scPP, or scAB) across different sample groups. Supports both single and multiple screen types visualization.

Usage

ScreenFractionPlot(
  screened_seurat,
  group_by = "Source",
  screen_type = c("scissor", "scPAS", "scPP", "scAB"),
  show_null = FALSE,
  plot_color = NULL,
  show_plot = TRUE,
  plot_title = "Screen Fraction",
  stack_width = 0.85,
  x_text_angle = 45,
  axis_linewidth = 0.8,
  legend_position = "right",
  x_lab = NULL,
  y_lab = "Fraction of Status",
  ncol = 2,
  nrow = NULL,
  scales = "fixed"
)

Arguments

screened_seurat

A Seurat object containing screening results in metadata. Must contain columns corresponding to screen_type.

group_by

Metadata column name for grouping samples (default: "Source").

screen_type

Screening algorithm(s) used. Can be a single value or vector. Must match metadata column(s) (case-sensitive, e.g., "scissor" for Scissor results).

show_null

Logical whether to show groups with zero cells (default: FALSE).

plot_color

Custom color palette (named vector format): - Required names: "Positive", "Negative", "Neutral" - Default: c("Neutral"="#CECECE", "Positive"="#ff3333", "Negative"="#386c9b")

show_plot

Logical to immediately display plot (default: TRUE).

plot_title

Plot title (default: "Screen Fraction"). When multiple screen types, can be a vector of titles or single title (will append screen type).

stack_width

Bar width (default: 0.85).

x_text_angle

X-axis label angle (default: 45).

axis_linewidth

Axis line thickness (default: 0.8).

legend_position

Legend position (default: "right").

x_lab

X-axis label (default: NULL).

y_lab

Y-axis label (default: "Fraction of Status").

ncol

Number of columns for facet wrap when multiple screen types (default: 2).

nrow

Number of rows for facet wrap when multiple screen types (default: NULL).

scales

Should scales be fixed ("fixed"), free ("free"), or free in one dimension ("free_x", "free_y") for faceted plots (default: "fixed").

Value

A list containing:

  • stats: A data frame (single screen) or list of data frames (multiple screens) with screening statistics including:

    • Grouping variable counts

    • Raw cell counts

    • Percentage fractions

  • plot: A ggplot2 object (single screen) or list of ggplot2 objects (multiple screens)

  • combined_plot: A combined plot using patchwork (only for multiple screens)

Visualization Details

  • Bars are ordered by descending Positive fraction

  • Y-axis shows percentage (0-100%)

  • Zero-fraction groups are automatically hidden unless show_null=TRUE

  • For multiple screen types, plots can be combined using patchwork

Examples

if (FALSE) { # \dontrun{
# Single screen type usage
res <- ScreenFractionPlot(
  screened_seurat = scissor_result,
  group_by = "PatientID",
  screen_type = "scissor"
)

# Multiple screen types at once
multi_res <- ScreenFractionPlot(
  screened_seurat = multi_screened_result,
  group_by = "TissueType",
  screen_type = c("scissor", "scPAS", "scPP", "scAB"),
  ncol = 2
)
} # }