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Plots for metabolism pathway scoring

Source: R/MetabolismPlot.R
MetabolismPlot.Rd

Plots for metabolism pathway scoring

Usage

MetabolismPlot(
  srt = NULL,
  res = NULL,
  group.by = NULL,
  assay_name = "METABOLISM",
  ...,
  verbose = TRUE
)

Arguments

srt

A Seurat object containing the results of RunMetabolism.

res

GSVA results generated by RunGSVA function. If provided, 'srt' and 'group.by' are ignored.

group.by

A character vector specifying the grouping variable used in RunMetabolism.

assay_name

The name of the assay or tools slot containing metabolism results. Default is "METABOLISM".

...

Additional arguments passed to GSVAPlot.

verbose

Whether to print the message. Default is TRUE.

See also

RunMetabolism, EnrichmentPlot

Examples

data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
pancreas_sub <- RunMetabolism(
  pancreas_sub,
  db = c("KEGG", "REACTOME"),
  group.by = "CellType",
  species = "Mus_musculus",
  method = "AUCell"
)

ht1 <- MetabolismPlot(
  pancreas_sub,
  group.by = "CellType",
  plot_type = "heatmap",
  topTerm = 10,
  show_row_names = TRUE,
  width = 1,
  height = 2
)
ht1$plot

ht2 <- MetabolismPlot(
  pancreas_sub,
  group.by = "CellType",
  plot_type = "heatmap",
  n_split = 3,
  topTerm = 100,
  use_raster = TRUE,
  width = 1,
  height = 2
)
ht2$plot

MetabolismPlot(
  pancreas_sub,
  group.by = "CellType",
  db = "GO_BP",
  plot_type = "comparison",
  topTerm = 5
)

MetabolismPlot(
  pancreas_sub,
  group.by = "CellType",
  db = "GO_BP",
  group_use = "Ductal",
  plot_type = "bar",
  topTerm = 5
)

MetabolismPlot(
  pancreas_sub,
  group.by = "CellType",
  group_use = "Ductal",
  db = "GO_BP",
  plot_type = "network",
  topTerm = 3
)

MetabolismPlot(
  pancreas_sub,
  group.by = "CellType",
  group_use = "Ductal",
  db = "GO_BP",
  plot_type = "enrichmap"
)

MetabolismPlot(
  pancreas_sub,
  group.by = "CellType",
  group_use = "Ductal",
  plot_type = "wordcloud",
  word_type = "feature"
)

pancreas_sub <- RunMetabolism(
  pancreas_sub,
  assay_name = "METABOLISM",
  db = c("KEGG", "REACTOME"),
  species = "Mus_musculus"
)

FeatureDimPlot(
  pancreas_sub,
  assay = "METABOLISM",
  features = rownames(pancreas_sub[["METABOLISM"]])[1:2],
  reduction = "umap"
)

FeatureStatPlot(
  pancreas_sub,
  stat.by = rownames(pancreas_sub[["METABOLISM"]])[1:2],
  group.by = "CellType",
  assay = "METABOLISM"
)

ht <- GroupHeatmap(
  pancreas_sub,
  exp_legend_title = "Z-score",
  features = rownames(pancreas_sub[["METABOLISM"]])[1:10],
  group.by = "CellType",
  assay = "METABOLISM",
  width = 1,
  height = 2
)