Plot paired Alert System pathway responses
AlertHeatmap.RdPathways are selected independently on the positive and negative sides using
an evidence-aware priority metric. Tile color displays either the raw paired
pathway effect or its null-standardized value. Text annotations display
response prevalence (r) and directional consistency (c).
Usage
AlertHeatmap(
seurat_obj,
misc_name = "AlertSystem",
score_method = c("expression", "ucell"),
top_n = 5L,
side = c("both", "positive", "negative"),
select_by = c("widespread_priority", "focal_priority", "abs_effect", "null_z",
"robust_fraction", "response_rate"),
fill_by = c("effect", "null_z"),
reorder_by = c("effect", "select"),
scale_mode = c("none", "unit"),
unit_q = 0.9,
show_annotations = TRUE,
show_fdr = TRUE,
fdr_cutoff = 0.05,
fill_limits = NULL
)Arguments
- seurat_obj
Seurat object processed by
AlertSystemScore().- misc_name
Name of the Alert System state in
seurat_obj@misc.- score_method
Score channel:
"expression"or"ucell".- top_n
Number of pathways selected separately from each requested effect side.
- side
One of
"both","positive", or"negative".- select_by
Ranking metric:
"widespread_priority","focal_priority","abs_effect","null_z","robust_fraction", or"response_rate".- fill_by
Tile fill: raw
"effect"or calibrated"null_z".- reorder_by
Order selected pathways by mean effect or selection score.
- scale_mode
"none"retains the native response scale;"unit"divides by a robust magnitude and clips display values to[-1, 1].- unit_q
Quantile of absolute displayed values used by unit scaling.
- show_annotations
Display
randcin each tile.- show_fdr
Display
*when FDR is at or belowfdr_cutoff.- fdr_cutoff
FDR threshold for the symbol.
- fill_limits
Optional explicit symmetric or asymmetric fill limits.