plotTrajectoryHeatmap: Expression dynamic in heatmap

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

Expression dynamic in heatmap

Description

Displays variable-expression values along a trajectory direction with a smoothed heatmap (from left to right).

Usage

plotTrajectoryHeatmap(
  object,
  trajectory_name,
  of_sample = "",
  variables,
  method_gs = "mean",
  arrange_rows = "none",
  show_rownames = FALSE,
  show_colnames = FALSE,
  split_columns = TRUE,
  smooth_span = 0.5,
  verbose = TRUE,
  hm_colors = viridis::inferno(150),
  ...
)

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.
variables	The variables of interest specified as a character vector: Gene sets: Must be in getGeneSets() Genes: Must be in getGenes() All elements of the specified character vector must either belong to gene sets or to genes.
arrange_rows	Alter the way the rows of the heatmap are displayed in order to highlight patterns. Currently either 'maxima' or 'minima'.
show_rownames	Logical. If set to TRUE the variable elements will be displayed at the rownames of the heatmap.
split_columns	Logial. If set to TRUE the heatmap is vertically splitted according to the trajectory parts.
smooth_span	The amount of smoothing specified as a single numeric value.
verbose	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)
hm_colors	A vector of colors to be used.
...	Additional parameters given to pheatmap::pheatmap()

Value

A heatmap of class 'pheatmap'.

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