do_BarPlot {SCpubr}

Create Bar Plots.

Description

Create Bar Plots.

Usage

do_BarPlot(
  sample,
  group.by,
  order = FALSE,
  add.n = FALSE,
  add.n.face = "bold",
  add.n.expand = c(0, 1.15),
  add.n.size = 4,
  order.by = NULL,
  split.by = NULL,
  facet.by = NULL,
  position = "stack",
  font.size = 14,
  font.type = "sans",
  legend.position = "bottom",
  legend.title = NULL,
  legend.ncol = NULL,
  legend.nrow = NULL,
  legend.byrow = FALSE,
  axis.text.x.angle = 45,
  xlab = NULL,
  ylab = NULL,
  colors.use = NULL,
  flip = FALSE,
  plot.title = NULL,
  plot.subtitle = NULL,
  plot.caption = NULL,
  plot.grid = FALSE,
  grid.color = "grey75",
  grid.type = "dashed",
  plot.title.face = "bold",
  plot.subtitle.face = "plain",
  plot.caption.face = "italic",
  axis.title.face = "bold",
  axis.text.face = "plain",
  legend.title.face = "bold",
  legend.text.face = "plain",
  strip.text.face = "bold",
  return_data = FALSE
)

Arguments

sample

Seurat | A Seurat object, generated by CreateSeuratObject.

group.by

character | Metadata column to compute the counts of. Has to be either a character or factor column.

order

logical | Whether to order the results in descending order of counts.

add.n

logical | Whether to add the total counts on top of each bar.

add.n.face

character | Font face of the labels added by add.n.

add.n.expand

numeric | Vector of two numerics representing the start and end of the scale. Minimum should be 0 and max should be above 1. This basically expands the Y axis so that the labels fit when flip = TRUE.

• stack: Set the bars side by side, displaying the total number of counts. Uses position_stack.

• fill: Set the bars on top of each other, displaying the proportion of counts from the total that each group represents. Uses position_fill.

add.n.size

numeric | Size of the labels

order.by

character | When split.by is used, value of group.by to reorder the columns based on its value.

split.by

character | Metadata column to split the values of group.by by. If not used, defaults to the active idents.

facet.by

character | Metadata column to gather the columns by. This is useful if you have other overarching metadata.

position

character | Position function from ggplot2. Either stack or fill.

font.size

numeric | Overall font size of the plot. All plot elements will have a size relationship with this font size.

font.type

character | Base font family for the plot. One of:

• mono: Mono spaced font.

• serif: Serif font family.

• sans: Default font family.

legend.position

character | Position of the legend in the plot. One of:

• top: Top of the figure.

• bottom: Bottom of the figure.

• left: Left of the figure.

• right: Right of the figure.

• none: No legend is displayed.

legend.title

character | Title for the legend.

legend.ncol

numeric | Number of columns in the legend.

legend.nrow

numeric | Number of rows in the legend.

legend.byrow

logical | Whether the legend is filled by row or not.

axis.text.x.angle

numeric | Degree to rotate the X labels. One of: 0, 45, 90.

xlab, ylab

character | Titles for the X and Y axis.

colors.use

named_vector | Named vector of valid color representations (either name of HEX codes) with as many named colors as unique values of group.by. If group.by is not provided, defaults to the unique values of Idents. If not provided, a color scale will be set by default.

flip

logical | Whether to invert the axis of the displayed plot.

plot.title, plot.subtitle, plot.caption

character | Title, subtitle or caption to use in the plot.

plot.grid

logical | Whether to plot grid lines.

grid.color

character | Color of the grid in the plot. In heatmaps, color of the border of the cells.

grid.type

character | One of the possible linetype options:

• blank.

• solid.

• dashed.

• dotted.

• dotdash.

• longdash.

• twodash.

plot.title.face, plot.subtitle.face, plot.caption.face, axis.title.face, axis.text.face, legend.title.face, legend.text.face

character | Controls the style of the font for the corresponding theme element. One of:

• plain: For normal text.

• italic: For text in itallic.

• bold: For text in bold.

• bold.italic: For text both in itallic and bold.

strip.text.face

character | Controls the style of the font for the strip text. One of:

• plain: For normal text.

• italic: For text in itallic.

• bold: For text in bold.

• bold.italic: For text both in itallic and bold.

return_data

logical | Returns a data.frame with the count and proportions displayed in the plot.

Value

A ggplot2 object containing a Bar plot.

Examples

  # Check Suggests.
  value <- SCpubr:::check_suggests(function_name = "do_BarPlot", passive = TRUE)

  if (isTRUE(value)){
    # Consult the full documentation in https://enblacar.github.io/SCpubr-book/

    # Define your Seurat object.
    sample <- readRDS(system.file("extdata/seurat_dataset_example.rds", package = "SCpubr"))

    # Basic bar plot, horizontal.
    p1 <- SCpubr::do_BarPlot(sample = sample,
                             group.by = "seurat_clusters",
                             legend.position = "none",
                             plot.title = "Number of cells per cluster")

    # Split by a second variable.
    sample$modified_orig.ident <- sample(x = c("Sample_A", "Sample_B", "Sample_C"),
                                         size = ncol(sample),
                                         replace = TRUE,
                                         prob = c(0.2, 0.7, 0.1))

    p <- SCpubr::do_BarPlot(sample,
                            group.by = "seurat_clusters",
                            split.by = "modified_orig.ident",
                            plot.title = "Number of cells per cluster in each sample",
                            position = "stack")


  } else if (base::isFALSE(value)){
    message("This function can not be used without its suggested packages.")
    message("Check out which ones are needed using `SCpubr::state_dependencies()`.")
  }