Plot several surface plots colored by numeric variables

Displays a surface plot for every variable specified in argument color_by.

plotSurfaceComparison() Takes the SPATA2 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, ...)

# S4 method for class 'SPATA2'
plotSurfaceComparison(
  object,
  color_by,
  alpha_by = FALSE,
  method_gs = NULL,
  normalize = TRUE,
  smooth = FALSE,
  smooth_span = NULL,
  pt_size = NULL,
  pt_alpha = NULL,
  pt_clrsp = NULL,
  display_image = NULL,
  bcsp_rm = NULL,
  na_rm = TRUE,
  outline = FALSE,
  outline_coords = NULL,
  outline_fct = c(1.75, 2.75),
  use_scattermore = NULL,
  sctm_pixels = c(1024, 1024),
  sctm_interpolate = FALSE,
  order = TRUE,
  order_desc = FALSE,
  xrange = getCoordsRange(object)$x,
  yrange = getCoordsRange(object)$y,
  verbose = NULL,
  ...
)

# S4 method for class 'data.frame'
plotSurfaceComparison(
  object,
  color_by,
  alpha_by = FALSE,
  pt_alpha = 0.9,
  pt_clrsp = "inferno",
  pt_size = 2,
  image = NULL,
  use_scattermore = FALSE,
  sctm_pixels = c(1024, 1024),
  sctm_interpolate = FALSE,
  bcsp_rm = NULL,
  na_rm = TRUE,
  order = TRUE,
  order_desc = FALSE,
  verbose = TRUE,
  ...
)

Arguments

...: Additional arguments given to ggplot2::facet_wrap().
alpha_by: Here, logical value. If TRUE, alpha of points is scaled to gene expression values in addition to the color of points.
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: Numeric value. Specifies the size of all points.
pt_alpha: Numeric value. Specifies the degree of transparency of all points.
pt_clrsp: The color spectrum to be used if the specified variable displayed by color is continuous. Run validColorSpectra() to see valid input.
display_image: Logical. If set to TRUE the histology image of the specified sample is displayed underneath the plot.
image: An image of class Image to be displayed in the background as obtained by getImage().