plotTrajectory: Plot trajectory

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

Plot trajectory

Description

Displays the spatial course of spatial trajectory that was drawn with SPATA::createTrajectories().

Usage

plotTrajectory(
  object,
  trajectory_name,
  of_sample = "",
  color_to = NULL,
  method_gs = "mean",
  smooth = FALSE,
  smooth_span = 0.02,
  pt_size = 2.5,
  pt_alpha = 0.4,
  pt_clr = "red",
  pt_clrp = "milo",
  pt_clrsp = "inferno",
  sgmt_size = 1,
  display_image = TRUE,
  display_title = FALSE,
  uniform_genes = "discard",
  verbose = TRUE
)

Arguments

object	A valid spata-object.
trajectory_name	The trajectory of interest specified as a single character value.
of_sample	The sample(s) of interest specified as a single character value or vector. If set to "" (the default) the first sample is chosen.
color_to	The variable to be displayed by color: Gene set as a single character value. Must be in getGeneSets() Genes as a character vector. If more than one gene is specified the average expression of those genes will be calculated and displayed. Must be in getGenes() Feature as a single character value. Must be in getFeaturenNames()
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_clr	The base color of every point displayed in the plot.
pt_clrp	The color panel to be used if the specified variable displayed by color is categorical/discrete. Run all_colorpanels() to see valid input.
pt_clrsp	The color spectrum to be used if the specified variable displayed by color is continuous. Run all_colorspectra() to see valid input..
sgmt_size	The size of the segment arrrow specified as a numeric value.
display_image	Logical. If set to TRUE the histology image of the specified sample is displayed underneath the plot.
display_title	Logical. If set to TRUE an informative title is displayed.
uniform_genes	Character value. If set to 'discard' genes that are uniformly expressed across all barcode-spots of the specified coordinates data.frame are discarded. If set to 'keep' they are kept.
verbose	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)

Value

Returns a ggplot-object that can be additionally customized according to the rules of the ggplot2-framework.

kueckelj/SPATA documentation built on March 22, 2022, 9:59 p.m.