plotSurfaceComparison: Plot several surface plots colored by numeric variables

In kueckelj/SPATA2: A Toolbox for Spatial Gene Expression Analysis

Plot several surface plots colored by numeric variables

Description

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.

Usage

plotSurfaceComparison(
  object,
  color_by,
  alpha_by = FALSE,
  method_gs = NULL,
  normalize = NULL,
  smooth = FALSE,
  smooth_span = NULL,
  pt_size = NULL,
  pt_alpha = NULL,
  pt_clrsp = NULL,
  display_image = NULL,
  bcsp_rm = NULL,
  na_rm = TRUE,
  use_scattermore = FALSE,
  sctm_pixels = c(1024, 1024),
  sctm_interpolate = FALSE,
  order = TRUE,
  order_desc = FALSE,
  verbose = NULL,
  ...
)

plotSurfaceComparison2(
  coords_df,
  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

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.
...	Additional arguments given to ggplot2::facet_wrap().
image	An image of class Image to be displayed in the background. Easily accessible via SPATA::image().

kueckelj/SPATA2 documentation built on March 16, 2024, 10:25 a.m.