sampleEnrichmentDotplot: Make a dot-plot of geneset enrichments across multiple...
In sansomlab/gsfisher: Geneset Fisher

sampleEnrichmentDotplot

R Documentation

Make a dot-plot of geneset enrichments across multiple samples/clusters

Description

Make a dot-plot of geneset enrichments across multiple samples/clusters

Usage

sampleEnrichmentDotplot(
  results_table,
  p_col = "p.adj",
  pvalue_threshold = 0.05,
  selected_genesets = c(),
  selection_col = "description",
  sample_id_col = "cluster",
  sample_levels = NULL,
  fill_var = "odds.ratio",
  fill_trans = "log2",
  fill_colors = c("yellow", "red", "brown"),
  fill_max_quantile = 1,
  non_significant_color = "grey90",
  min_dot_size = 2,
  max_dot_size = 8,
  maxl = Inf,
  rotate_sample_labels = FALSE,
  title = NULL
)

Arguments

`results_table`	The results table
`p_col`	The name of the column with the (e.g. adjusted) p-values
`pvalue_threshold`	The pvalue_threshold to be applied
`selected_genesets`	A vector of geneset slow in the plot
`selection_col`	The column against which the geneset selections will be matched
`sample_id_col`	The column of the results_table containing the sample id
`fill_var`	The column to use for the fill color.
`fill_trans`	Name of the transformation for the fill. "-log10" is supported for p-values.
`fill_colors`	Colors for the fill gradient
`fill_max_quantile`	The quantile at which (non-infinite) fill variable will be capped for the color scale.
`min_dot_size`	Minimum dot size (points)
`max_dot_size`	Maximum dot size (points)
`maxl`	The maximum length for the geneset labels
`rotate_sample_labels`	Should the sample labels be rotated