plotTrajectoryHeatmap: Plot trajectory expression dynamic in heatmap
In kueckelj/SPATA2: A Toolbox for Spatial Gene Expression Analysis

plotTrajectoryHeatmap

R Documentation

Plot trajectory expression dynamic in heatmap

Description

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

Usage

plotTrajectoryHeatmap(
  object,
  id,
  variables,
  binwidth = getCCD(object),
  n_bins = NA_integer_,
  arrange_rows = "none",
  colors = NULL,
  method_gs = NULL,
  show_rownames = NULL,
  show_colnames = NULL,
  split_columns = NULL,
  smooth_span = NULL,
  multiplier = 10,
  with_ggplot = TRUE,
  display_parts_with = "lines",
  line_alpha = 1,
  line_color = "red",
  line_size = 1,
  line_type = "dashed",
  clrsp = NULL,
  .f = NULL,
  .cols = dplyr::everything(),
  summarize_with = "mean",
  verbose = NULL,
  ...
)

Arguments

`object`	An object of class `spata2`.
`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.
`binwidth`	Numeric value. Denotes the binwidth with which to sort all relevant barcode spots into groups that are then aligned with respect to the chosen trajectory's direction.#'
`n_bins`	Numeric value. Specifies the exact number of bins the barcodes are binned into.
`arrange_rows`	Alter the way the rows of the heatmap are displayed in order to highlight patterns. Currently either 'maxima', 'minima' or 'input'. If 'input', variables are displayed in the same order as they are provided in the argument `variables`.
`colors`	A vector of colors to be used.
`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().
`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`	Numeric value. Controls the degree of smoothing. Given to argument `span` of `stats::loess()`.
`multiplier`	Numeric value. For better visualization the transient pattern is smoothed with a loess fit. The total number of predicted values (via `stats::predict()`) is the number of bins multiplied with the input for this argument.
`with_ggplot`	Logical value. If set to TRUE the heatmap is plotted with `ggplot2::geom_tile()` and a ggplot is returned.
`display_parts_with`	Character value. Either 'facets' or 'lines'.
`line_alpha`	Numeric value. Specifies the transparency of the lines.
`line_color`	Character. Affects color of the main lines of the plot.
`line_size`	Numeric. Affects size of the main lines of the plot.
`line_type`	Character. The line type. One of 'blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash' and 'twodash'.
`clrsp`	Character value. Specifies the color spectrum to be used to represent continuous values of numeric variables. Run `validColorSpectra()` to obtain valid input options.
`summarize_with`	Character value. Name of the function with which to summarize.
`verbose`	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)
`...`	Additional parameters given to `pheatmap::pheatmap()`. If argument `with_ggplot` is TRUE given to `scale_color_add_on()`.
`display_trajectory_parts`	Logical value. If TRUE and the trajectory contains more than one part the parts are displayed by facetting the plot or by adding vertical lines.