hlpr_scatterplot: Color to + scatterplot helper

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

Color to + scatterplot helper

Description

Color to + scatterplot helper

Usage

hlpr_scatterplot(
  object,
  spata_df,
  color_to,
  method_gs = "mean",
  display_title = FALSE,
  pt_size = 2,
  pt_alpha = 1,
  pt_clrsp = "inferno",
  pt_clrp = "milo",
  pt_clr = "black",
  smooth = FALSE,
  smooth_span = 0.02,
  normalize = TRUE,
  verbose = TRUE,
  complete = FALSE,
  ...
)

Arguments

object	An object of class spata2.
color_to	Named list.
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 TRUE, a loess fit is used to smooth the values.
smooth_span	Numeric value. Controls the degree of smoothing. Given to argument span of stats::loess().
normalize	Logical. If set to TRUE values will be scaled to 0-1. Hint: Variables that are uniformly expressed can not be scaled and are discarded.
verbose	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)

Value

A named list. Slot data contains a data.frame as input for data of ggplot2::ggplot() and slot add_on contains a list of ggplot-add-ons.

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