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
)Returns a ggplot2 object
A Seurat object
Name of key to pull data from. Stores the results from
RegionMatrix
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
Cell identities to include. Note that cells cannot be
regrouped, this will require re-running RegionMatrix to generate a
new set of matrices
Normalize by number of cells in each group
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
Number of bases to include downstream of region. See
documentation for upstream
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
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.
Minimum total counts to display region in plot
Smoothing window to apply
Order regions by the total number of fragments in the region across all included identities
Number of rows to use when creating plot. If NULL, chosen automatically by ggplot2
RegionMatrix