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,
  group_use = NULL,
  DE_threshold = "avg_log2FC > 0 & p_val_adj < 0.05",
  group_palette = "Chinese",
  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,
  only.pos = FALSE,
  label.by = c("p_val_adj", "p_val", "diff_pct", "avg_log2FC"),
  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: A Seurat object or SummarizedExperiment object containing the results of differential expression analysis.
group.by: Metadata column(s) used to color cells.
test.use: Type of statistical test to use.
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.
group_use: Groups to plot. Default is NULL (all groups).
DE_threshold: Threshold for differential expression (used to highlight significant genes in all plot types). Default is "p_val < 0.05" for sample-level methods ("edgeR" and "limma"). For cell-level volcano plots, it is "abs(avg_log2FC) > 0 & p_val_adj < 0.05" when only.pos = FALSE, and "avg_log2FC > 0 & p_val_adj < 0.05" otherwise.
group_palette: Palette for cell types (groups) in Manhattan plot.
group_palcolor: Custom colors for cell types (groups) in Manhattan plot.
pt.size: The size of the points.
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.
cols.highlight: Color for highlighted points.
sizes.highlight: The size of the highlighted points.
alpha.highlight: The transparency of the highlighted points.
stroke.highlight: The stroke width for the highlighted points.
nlabel: An integer value specifying the number of labeled points per group.
features_label: Feature labels to plot.
only.pos: Whether to show only positive log2 fold-change results in differential expression visualizations.
label.by: Metric used to select automatic labels when features_label = NULL. Options are "p_val_adj", "p_val", "diff_pct", and "avg_log2FC". Smaller p-values are ranked first; diff_pct and avg_log2FC use the strongest positive and negative effects within each group.
label.fg: Color for the labels' foreground.
label.bg: Color for the labels' background.
label.bg.r: The radius of the rounding of the labels' background.
label.size: The size of the labels.
palette: Color palette name. Available palettes can be found in thisplot::show_palettes.
palcolor: Custom colors used to create a color palette.
theme_use, theme_args: Theme name or function, plus extra theme arguments.
tile_height: Height of the cell-type track in ring plot.
tile_gap: Gap between the track and nudged points in ring plot.
jitter_width: Horizontal jitter range for points in Manhattan plot.
ring_segments: Whether to draw segment lines between cell types in ring plot.
seed: Random seed for jitter in Manhattan and ring plots.

Examples

data(pancreas_sub)
pancreas_sub <- RunStandardWorkflow(pancreas_sub)
#> ℹ [2026-08-30 04:21:05] Start standard processing workflow...
#> ℹ [2026-08-30 04:21:05] Checking a list of <Seurat>...
#> ! [2026-08-30 04:21:05] Data 1/1 of the `srt_list` is "unknown"
#> Warning: Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2026-08-30 04:21:05] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on 1/1 of `srt_list`...
#> ℹ [2026-08-30 04:21:05] Perform `FindVariableFeatures()` on 1/1 of `srt_list`...
#> ℹ [2026-08-30 04:21:06] Use the separate HVF from `srt_list`
#> ℹ [2026-08-30 04:21:06] Number of available HVF: 2000
#> ℹ [2026-08-30 04:21:06] Finished check
#> ℹ [2026-08-30 04:21:06] Perform `ScaleData()`
#> ℹ [2026-08-30 04:21:06] Perform pca linear dimension reduction
#> ℹ [2026-08-30 04:21:06] Use stored estimated dimensions 1:23 for Standardpca
#> ℹ [2026-08-30 04:21:06] Perform `Seurat::FindClusters()` with `cluster_algorithm = 'louvain'` and `cluster_resolution = 0.6`
#> ℹ [2026-08-30 04:21:07] Reorder clusters...
#> ℹ [2026-08-30 04:21:07] Skip `log1p()` because `layer = data` is not "counts"
#> ℹ [2026-08-30 04:21:07] Perform umap nonlinear dimension reduction
#> ✔ [2026-08-30 04:21:14] Standard processing workflow completed
pancreas_sub <- RunDEtest(
  pancreas_sub,
  group.by = "CellType",
  only.pos = FALSE
)
#> ℹ [2026-08-30 04:21:14] Data type is log-normalized
#> ℹ [2026-08-30 04:21:14] Start differential expression test
#> ℹ [2026-08-30 04:21:14] Find all markers(wilcox) among [1] 5 groups...
#> ✔ [2026-08-30 04:21:14] Differential expression test completed
DEtestRingPlot(
  pancreas_sub,
  group.by = "CellType"
)

Usage

Arguments

See also

Examples