ClusterUMAPthresholding: ClusterUMAPthresholding

In jn-goe/gruffi: Gruffi identifies and removes stressed cells from brain organoid single-cell datasets.

ClusterUMAPthresholding

Description

clUMAP with threshold value.

Usage

ClusterUMAPthresholding(
  q.meta.col = "Score.GO.0034976",
  c.meta.col = "integrated_snn_res.30",
  quantile = 0.95,
  absolute.cutoff = NULL,
  obj = combined.obj,
  plot.barplot = FALSE,
  subt = "response to ER stress",
  plotUMAP = TRUE,
  ...
)

Arguments

q.meta.col	Numeric metadata column name, Default: 'Score.GO.0034976'
c.meta.col	Clustering basis to split the data (Categorical metadata column name), Default: 'integrated_snn_res.30'
quantile	Quantile, Default: 0.95
absolute.cutoff	Absolute cutoff, Default: NULL
obj	Seurat single cell object, Default: combined.obj
plot.barplot	Draw a barplot? Default: FALSE
subt	Plot Subtitle, Default: 'response to ER stress'
plotUMAP	Draw a UMAP? Default: TRUE
...	Pass any other parameter to the internally called functions (most of them should work).

See Also

calc.cluster.averages

jn-goe/gruffi documentation built on Nov. 7, 2024, 10:38 p.m.