Plot several surface plots at the same time — plotSurfaceComparison • SPATA

Plots a surface plot for every valid element in argument variables and colors it according to each element.

plotSurfaceComparison() Takes the spata-object as the starting point and creates the necessary data.frame from scratch according to additional parameters.
plotSurfaceComparison2() Takes a data.frame as the starting point.

plotSurfaceComparison(
  object,
  of_sample = "",
  variables,
  method_gs = "mean",
  normalize = TRUE,
  smooth = FALSE,
  smooth_span = 0.02,
  pt_size = 2,
  pt_alpha = 1,
  pt_clrsp = "inferno",
  display_image = FALSE,
  assign = FALSE,
  assign_name,
  verbose = TRUE,
  ...
)

plotSurfaceComparison2(
  coords_df,
  variables = "all",
  pt_size = 2,
  pt_alpha = 0.9,
  pt_clrsp = "inferno",
  image = NULL,
  verbose = TRUE,
  ...
)

Arguments

variables	Character vector. The variables of interest: Gene sets: Must be in `getGeneSets()` Genes: Must be in `getGenes()` Features: Must be numeric ones of `getFeatureNames()`
method_gs	Character value. The method according to which gene sets will be handled specified as a character of length one. This can be either 'mean' or one of 'gsva', 'ssgsea', 'zscore', or 'plage'. The latter four will be given to `gsva::GSVA()`.
smooth	Logical. If set to TRUE values will be smoothed according to the `smoooth_`-parameters.
smooth_span	The amount of smoothing specified as a single numeric value.
pt_size	The size of the points specified as a single numeric value.
pt_alpha	The transparency of the points specified as single numeric value.
pt_clrsp	The color spectrum to be used if the specified variable displayed by color is continuous. Run `all_colorspectra()` to see valid input..
display_image	Logical. If set to TRUE the histology image of the specified sample is displayed underneath the plot.
assign	Logical. If set to TRUE a named list will be assigned to the global environment. This list contains data and information to rebuild or additionally customize the output plot of this function.
assign_name	The name the assigned list is supposed to have specified as a single character value.
verbose	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)
...	Additional arguments given to `ggplot2::facet_wrap()`.
image	An image of class Image to be displayed in the background. Easily accessible via `SPATA::image()`.
data	A data.frame containing the numeric variables of interest.