Region heatmap

Plot fragment counts within a set of regions.

RegionHeatmap(
  object,
  key,
  assay = NULL,
  idents = NULL,
  normalize = TRUE,
  upstream = 3000,
  downstream = 3000,
  max.cutoff = "q95",
  cols = NULL,
  min.counts = 1,
  window = (upstream + downstream)/30,
  order = TRUE,
  nrow = NULL
)

Arguments

object: A Seurat object
key: Name of key to pull data from. Stores the results from RegionMatrix
assay: Name of assay to use. If a list or vector of assay names is given, data will be plotted from each assay. Note that all assays must contain RegionMatrix results with the same key. Sorting will be defined by the first assay in the list
idents: Cell identities to include. Note that cells cannot be regrouped, this will require re-running RegionMatrix to generate a new set of matrices
normalize: Normalize by number of cells in each group
upstream: Number of bases to include upstream of region. If NULL, use all bases that were included in the RegionMatrix function call. Note that this value cannot be larger than the value for upstream given in the original RegionMatrix function call. If NULL, use parameters that were given in the RegionMatrix function call
downstream: Number of bases to include downstream of region. See documentation for upstream
max.cutoff: Maximum cutoff value. Data above this value will be clipped to the maximum value. A quantile maximum can be specified in the form of "q##" where "##" is the quantile (eg, "q90" for 90th quantile). If NULL, no cutoff will be set
cols: Vector of colors to use as the maximum value of the color scale. One color must be supplied for each assay. If NULL, the default ggplot2 colors are used.
min.counts: Minimum total counts to display region in plot
window: Smoothing window to apply
order: Order regions by the total number of fragments in the region across all included identities
nrow: Number of rows to use when creating plot. If NULL, chosen automatically by ggplot2

Value

Returns a ggplot2 object

Arguments

Value

See also