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Bar plot of the cell proportions in each identity

Source: R/Barplot_Cell_Proportion.R
Barplot_Cell_Proportion.Rd

This function generates a bar plot of the cell proportions from a Seurat object.

Usage

Barplot_Cell_Proportion(
  seurat_object,
  group.by = NULL,
  split.by = NULL,
  idents = NULL,
  group.idents = NULL,
  split.idents = NULL,
  colors = NULL,
  order.prop = NULL,
  order.group = NULL,
  order.split = NULL,
  order.colors = TRUE,
  alpha = 1,
  show.cellsum.label = TRUE,
  cellsum.label.size = 3,
  axis.text.size = 9,
  x.axis.angle = 60,
  x.axis.hjust = 1,
  y.axis.title.size = 11,
  legend.text.size = 9,
  legend.side = "bottom",
  show.legend = TRUE,
  split.plot.title.size = 24,
  prop.percent = TRUE,
  nrow = 1,
  unique.group.plot = TRUE,
  unique.split.plot = FALSE,
  output.data = FALSE
)

Arguments

seurat_object

A Seurat object.

group.by

Character. The name of a metadata (for example, 'orig.ident', 'seurat_clusters', etc) to group the identities of the active.ident metadata by. Returns a stacked bar plot.

split.by

Character. The name of a metadata to split the identities of the active.ident metadata by. Returns separate ggplot2 objects.

idents

Character. The names of one or several identities in the active.ident metadata to select. If NULL, all identities are used.

group.idents

Character. The names of one or several group.by identities to select. If NULL, all identities are used. Ignored if group.by = NULL.

split.idents

Character. The names of one or several split.by identities to select. If NULL, all identities are used. Ignored if split.by = NULL.

colors

Character. The color names for each identity of the active.ident metadata or in idents. If NULL, uses Seurat's default colors.

order.prop

Character or Numeric. Either 'reverse', or the identities (as names or as numeric values corresponding to the indices) of the active.ident metadata or in idents to order the cells.

order.group

Character. Either 'reverse', or the names of the group.by identities or in group.idents to order the cells. Ignored if group.by = NULL.

order.split

Character. Either 'reverse', or the names of the split.by identities or in split.idents to order the cells. Ignored if split.by = NULL.

order.colors

Logical. If TRUE, the colors will automatically be ordered according to order.prop. Ignored if order.prop = NULL.

alpha

Numeric. The transparency of the bar colors. A value between 0 and 1.

show.cellsum.label

Logical. If TRUE, the cell sum will be shown at the top of each bar.

cellsum.label.size

Numeric. The font size of the cell sum label. Ignored if show.cellsum.label = FALSE.

axis.text.size

Numeric. The font size of the identity names and cell percent or count.

x.axis.angle

Numeric. The rotation angle of the identity names.

x.axis.hjust

Numeric. The horizontal justification of the identity names.

y.axis.title.size

Numeric. The font size of the y axis title.

legend.text.size

Numeric. The font size of the legend text. Ignored if show.legend = FALSE.

legend.side

Character. The side where the legend will be displayed, either 'left', 'right', 'top' or 'bottom'. Ignored if show.legend = FALSE.

show.legend

Logical. If TRUE, shows the legend.

split.plot.title.size

Numeric. The font size of the split plot titles. Ignored if split.by = NULL.

prop.percent

Logical. If TRUE, the cell proportions will be shown as a percentage of total cells for each identity. Ignored if group.by = NULL.

nrow

Numeric. The number of rows in the patchwork object. Ignored if group.by = NULL and split.by = NULL.

unique.group.plot

Logical. If TRUE, the stacked bar plots will be gathered in a single ggplot2 object. Ignored if group.by = NULL.

unique.split.plot

Logical. If TRUE, the ggplot2 objects will be gathered in a single patchwork. Ignored if split.by = NULL.

output.data

Logical. If TRUE, the function will return a data.frame object or a list of data.frame objects of the cell proportions, instead of displaying anything.

Value

A ggplot2 object, a list of ggplot2 objects, a patchwork object containing ggplot2 objects or a list of patchwork objects containing ggplot2 objects.

Examples

# Prepare data
pbmc3k <- Right_Data("pbmc3k")

# Example 1: default parameters
Barplot_Cell_Proportion(pbmc3k)