plotTrajectoryFeatures: Trajectory line plots

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

Trajectory line plots

Description

Displays values along a trajectory direction with a smoothed lineplot.

Usage

plotTrajectoryFeatures(
  object,
  trajectory_name,
  of_sample = "",
  features = "percent.mt",
  smooth_method = "loess",
  smooth_span = 0.2,
  smooth_se = TRUE,
  clrp = "milo",
  verbose = TRUE
)

plotTrajectoryFeaturesDiscrete(
  object,
  trajectory_name,
  of_sample = "",
  discrete_feature,
  clrp = "milo",
  display_trajectory_parts = FALSE,
  verbose = TRUE,
  ...
)

plotTrajectoryGenes(
  object,
  trajectory_name,
  of_sample = "",
  genes,
  clrp = "milo",
  average_genes = FALSE,
  smooth_method = "loess",
  smooth_span = 0.2,
  smooth_se = TRUE,
  display_trajectory_parts = TRUE,
  verbose = TRUE
)

plotTrajectoryGeneSets(
  object,
  trajectory_name,
  of_sample = "",
  gene_sets = "Neftel_NPC_Comb",
  method_gs = "mean",
  smooth_method = "loess",
  smooth_span = 0.2,
  smooth_se = TRUE,
  clrp = "milo",
  display_trajectory_parts = TRUE,
  verbose = TRUE
)

Arguments

object	A valid spata-object.
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.
features	The features of interest specified as a character vector.
smooth_method	The smoothing method that will be used specified as a single character value (e.g. "lm", "glm", "gam", "loess").
smooth_span	The amount of smoothing specified as a single numeric value.
smooth_se	Logical. If set to TRUE the confidence interval will be displayed.
clrp	Character value. The color panel to be used. Run all_colorpanels() to see valid input.
verbose	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)
discrete_feature	Character value. The discrete feature of interest.
display_trajectory_parts	Logical. If set to TRUE the returned plot visualizes the parts in which the trajectory has been partitioned while beeing drawn.
genes	The genes of interest specified as a character vector.
average_genes	Logical value. If set to TRUE the mean expression of all specified genes will be calculated.
gene_sets	The gene sets of interest specified as a character vector.
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().

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.