DEtest Ring Plot

Draw a circular (ring) plot of differential expression results by cell type.

Usage

DEtestRingPlot(
  srt,
  group.by = NULL,
  test.use = "wilcox",
  res = NULL,
  DE_threshold = "avg_log2FC > 0 & p_val_adj < 0.05",
  group_palette = "Paired",
  group_palcolor = NULL,
  pt.size = 1,
  pt.alpha = 1,
  cols.highlight = "black",
  sizes.highlight = 1,
  alpha.highlight = 1,
  stroke.highlight = 0.5,
  nlabel = 5,
  features_label = NULL,
  label.fg = "black",
  label.bg = "white",
  label.bg.r = 0.1,
  label.size = 4,
  palette = "RdBu",
  palcolor = NULL,
  theme_use = "theme_scop",
  theme_args = list(),
  tile_height = 0.3,
  tile_gap = 0.1,
  jitter_width = 0.5,
  ring_segments = TRUE,
  seed = 11
)

Arguments

srt: An object of class Seurat containing the results of differential expression analysis.
group.by: Name of one or more meta.data columns to group (color) cells by.
test.use: A character string specifying the type of statistical test to use. Default is "wilcox".
res: A data.frame or data.table with differential expression results. When res is provided, srt will be ignored. The data.frame must contain columns: gene, group1 (factor or character), avg_log2FC, p_val_adj, and optionally pct.1 and pct.2 for calculating diff_pct.
DE_threshold: A character string specifying the threshold for differential expression (used to highlight significant genes in all plot types). Default is "avg_log2FC > 0 & p_val_adj < 0.05".
group_palette: Palette for cell types (groups) in Manhattan plot. Default is "Paired".
group_palcolor: Custom colors for cell types (groups) in Manhattan plot. Default is NULL.
pt.size: The size of the points. Default is 1.
pt.alpha: The transparency of the data points. Default is 1.
cols.highlight: A character string specifying the color for highlighted points. Default is "black".
sizes.highlight: The size of the highlighted points. Default is 1.
alpha.highlight: The transparency of the highlighted points. Default is 1.
stroke.highlight: The stroke width for the highlighted points. Default is 0.5.
nlabel: An integer value specifying the number of labeled points per group. Default is 5.
features_label: A character vector specifying the feature labels to plot. Default is NULL.
label.fg: A character string specifying the color for the labels' foreground. Default is "black".
label.bg: A character string specifying the color for the labels' background. Default is "white".
label.bg.r: The radius of the rounding of the labels' background. Default is 0.1.
label.size: The size of the labels. Default is 4.
palette: Color palette name. Available palettes can be found in thisplot::show_palettes. Default is "RdBu".
palcolor: Custom colors used to create a color palette. Default is NULL.
theme_use: Theme to use for the plot. Default is "theme_scop".
theme_args: A list of additional arguments to pass to the theme function. Default is list().
tile_height: Height of the cell-type track in ring plot. Default is 0.3.
tile_gap: Gap between the track and nudged points in ring plot. Default is 0.1.
jitter_width: Horizontal jitter range for points in Manhattan plot. Default is 0.5.
ring_segments: Whether to draw segment lines between cell types in ring plot. Default is TRUE.
seed: Random seed for jitter in ring plot. Default is 11.

Examples

data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
#> ℹ [2026-02-11 03:16:33] Start standard scop workflow...
#> ℹ [2026-02-11 03:16:34] Checking a list of <Seurat>...
#> ! [2026-02-11 03:16:34] Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2026-02-11 03:16:34] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on the data 1/1 of the `srt_list`...
#> ℹ [2026-02-11 03:16:36] Perform `Seurat::FindVariableFeatures()` on the data 1/1 of the `srt_list`...
#> ℹ [2026-02-11 03:16:36] Use the separate HVF from srt_list
#> ℹ [2026-02-11 03:16:36] Number of available HVF: 2000
#> ℹ [2026-02-11 03:16:36] Finished check
#> ℹ [2026-02-11 03:16:37] Perform `Seurat::ScaleData()`
#> ℹ [2026-02-11 03:16:37] Perform pca linear dimension reduction
#> ℹ [2026-02-11 03:16:38] Perform `Seurat::FindClusters()` with `cluster_algorithm = 'louvain'` and `cluster_resolution = 0.6`
#> ℹ [2026-02-11 03:16:38] Reorder clusters...
#> ℹ [2026-02-11 03:16:38] Perform umap nonlinear dimension reduction
#> ℹ [2026-02-11 03:16:38] Non-linear dimensionality reduction (umap) using (Standardpca) dims (1-50) as input
#> ℹ [2026-02-11 03:16:41] Non-linear dimensionality reduction (umap) using (Standardpca) dims (1-50) as input
#> ✔ [2026-02-11 03:16:44] Run scop standard workflow completed
pancreas_sub <- RunDEtest(
  pancreas_sub,
  group.by = "CellType",
  only.pos = FALSE
)
#> ℹ [2026-02-11 03:16:44] Data type is log-normalized
#> ℹ [2026-02-11 03:16:44] Start differential expression test
#> ℹ [2026-02-11 03:16:44] Find all markers(wilcox) among [1] 5 groups...
#> ℹ [2026-02-11 03:16:44] Using 1 core
#> ⠙ [2026-02-11 03:16:44] Running for Ductal [1/5] ■■■■■■■                       …
#> ✔ [2026-02-11 03:16:44] Completed 5 tasks in 895ms
#> 
#> ℹ [2026-02-11 03:16:44] Building results
#> ✔ [2026-02-11 03:16:45] Differential expression test completed
DEtestRingPlot(
  pancreas_sub,
  group.by = "CellType"
)

Usage

Arguments

See also

Examples