Plot Expression Heatmap — plotExpressionHeatmap • SpatialMap

This function takes a SpatialMap or Region object and plots biomarker expression values in a heatmap.

Usage

plotExpressionHeatmap(
  object,
  data.slot = "NormalizedData",
  summary.fun = "mean",
  summarize.across = ".clusters",
  exclude.markers = NULL,
  subsample = TRUE,
  color.pal = NULL,
  remove = c("na", "inf", "nan"),
  trim = "all",
  cuts = c(0.01, 0.99),
  scaling = "row",
  name = "Marker\nexpression",
  column_title = sprintf("Marker expression by `%s`", summarize.across),
  row_names_gp = grid::gpar(fontsize = 7),
  bottom_pad = 0.2,
  left_pad = 0.2,
  top_pad = 0.2,
  right_pad = 0.5,
  pad_units = "cm",
  ...
)

Arguments

object: A SpatialMap or Region object.
data.slot: Which data slot to use.
summary.fun: How to summarize the cells specified by summarize.across groups. Should be the name of a function given as a string.
summarize.across: Groups to summarize data values across using summary.fun. Can be the name of any column in cellMetadata.
exclude.markers: Specific markers to exclude from the heatmap. If NULL, does nothing.
subsample: Whether or not to subsample cells if there are more than 10,000 cells.
color.pal: A vector of colors.
remove: Character or char vector describing classes to remove, e.g. na, inf, nan
trim: How to trim quantiles - rowwise ("row"), colwise ("col"), or in whole matrix ("all").
cuts: Quantile values to cut. If NULL, trim will not happen.
scaling: Character describing the style of scaling to employ
name: ComplexHeatmap::Heatmap() argument. The legend title -- what is plotted in the heatmap?
column_title: ComplexHeatmap::Heatmap() argument. Title at the top of the heatmap.
row_names_gp: ComplexHeatmap::Heatmap() Graphical parameters to row names. Argument must be a call to grid::gpar().
bottom_pad: Padding to add to bottom of plot. Useful if text is getting cut off.
left_pad: Padding to add to left side of plot. Useful if text is getting cut off.
top_pad: Padding to add to top of plot. Useful if text is getting cut off.
right_pad: Padding to add to right side of plot. Useful if text is getting cut off.
pad_units: What units of measurement should the padding values be interpreted as? See ?grid::unit for a list of allowed values.
...: Additional arguments passed to ComplexHeatmap::Heatmap()

Examples

if (FALSE) {
  sm <- load_sm_data(dataset = "skin")
  # With all features
  plts <- plotExpressionHeatmap(
    sm,
    data.slot = "Data",
    summarize.across = "cell_type"
  )
  print(plts)
  # With excluding features
  exclude_features <- tail(features(sm), n = -3)
  plts_2 <- plotExpressionHeatmap(
    sm,
    data.slot = "Data",
    summarize.across = "cell_type",
    exclude.markers = exclude_features
  )
  print(plts_2)
}