stack_plot: Stacked bar plot

In cellGeometry: Geometric Single Cell Deconvolution

Stacked bar plot

Description

Produces stacked bar plots using base graphics or ggplot2 showing amounts of cell subclasses in deconvoluted bulk samples.

Usage

stack_plot(
  x,
  percent = FALSE,
  order_col = 1,
  scheme = NULL,
  order_cells = c("none", "increase", "decrease"),
  seriate = NULL,
  cex.names = 0.7,
  show_xticks = TRUE,
  ...
)

stack_ggplot(
  x,
  percent = FALSE,
  order_col = 1,
  scheme = NULL,
  order_cells = c("none", "increase", "decrease"),
  seriate = NULL,
  legend_ncol = NULL,
  legend_position = "bottom",
  show_xticks = FALSE
)

Arguments

x	matrix of deconvolution results with samples in rows and cell subclasses or groups in columns. If a 'deconv' class object is supplied the deconvolution values for the cell subclasses are extracted and plotted.
percent	Logical whether to scale the matrix rows as percentage.
order_col	Numeric value for which column (cell subclass) to use to sort the bars - this only applies if percent = TRUE. If a vector of column indices is supplied, these columns are averaged first using rowMeans(). If percent = FALSE, then the default is to sort bars from low to high based on the row sums (i.e. total subclass cell amounts in each sample). Setting order_col = 0 disables sorting of bars; in this case bars are shown in the original order of the rows of x.
scheme	Vector of colours. If not supplied, the default scheme uses scales::hue_pal().
order_cells	Character value specifying with cell types are ordered by abundance.
seriate	Character value which enables ordering of samples using the seriation package. Any matrix based seriation methods can be used to order the samples. Recommended options include "CA", "BEA" or "BEA_TSP".
cex.names	Character expansion controlling bar names font size.
show_xticks	Logical whether to show rownames as x axis labels.
...	Optional arguments passed to graphics::barplot().
legend_ncol	Number of columns for ggplot2 legend. If set to NULL ggplot2 sets the column number automatically.
legend_position	Position of ggplot2 legend

Value

The base graphics function has no return value. It plots a stacked barchart using base graphics. The ggplot2 version returns a ggplot2 object.

cellGeometry documentation built on April 20, 2026, 1:06 a.m.