do_BoxPlot: Generate Box Plots.

In enblacar/SCpubr: Generate Publication Ready Visualizations of Single Cell Transcriptomics Data

Generate Box Plots.

Description

Generate Box Plots.

Usage

do_BoxPlot(
  sample,
  feature,
  group.by = NULL,
  split.by = NULL,
  assay = NULL,
  slot = "data",
  font.size = 14,
  font.type = "sans",
  axis.text.x.angle = 45,
  colors.use = NULL,
  na.value = "grey75",
  plot.title = NULL,
  plot.subtitle = NULL,
  plot.caption = NULL,
  xlab = NULL,
  ylab = NULL,
  legend.title = NULL,
  legend.title.position = "top",
  legend.position = "bottom",
  legend.ncol = NULL,
  legend.nrow = NULL,
  legend.byrow = FALSE,
  boxplot.line.color = "black",
  outlier.color = "black",
  outlier.alpha = 0.5,
  boxplot.linewidth = 0.5,
  boxplot.width = NULL,
  plot.grid = TRUE,
  grid.color = "grey75",
  grid.type = "dashed",
  flip = FALSE,
  order = FALSE,
  use_silhouette = FALSE,
  use_test = FALSE,
  comparisons = NULL,
  test = "wilcox.test",
  map_signif_level = c(`***` = 0.001, `**` = 0.01, `*` = 0.05),
  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"
)

Arguments

sample	Seurat | A Seurat object, generated by CreateSeuratObject.
feature	character | Feature to represent.
group.by	character | Metadata variable to group the output by. Has to be a character of factor column.
split.by	character | Secondary metadata variable to further group (split) the output by. Has to be a character of factor column.
assay	character | Assay to use. Defaults to the current assay.
slot	character | Data slot to use. Only one of: counts, data, scale.data. Defaults to "data".
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.
axis.text.x.angle	numeric | Degree to rotate the X labels. One of: 0, 45, 90.
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.
na.value	character | Color value for NA.
plot.title, plot.subtitle, plot.caption	character | Title, subtitle or caption to use in the plot.
xlab, ylab	character | Titles for the X and Y axis.
legend.title	character | Title for the legend.
legend.title.position	character | Position for the title of the legend. One of: top: Top of the legend. bottom: Bottom of the legend. left: Left of the legend. right: Right of the legend.
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.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.
boxplot.line.color	character | Color of the borders of the boxplots if use_silhouette is FALSE.
outlier.color	character | Color of the outlier dots.
outlier.alpha	numeric | Alpha applied to the outliers.
boxplot.linewidth	numeric | Width of the lines in the boxplots. Also controls the lines of the tests applied if use_test is set to true.
boxplot.width	numeric | Width of the boxplots.
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.
flip	logical | Whether to invert the axis of the displayed plot.
order	logical | Whether to order the boxplots by average values. Can not be used alongside split.by.
use_silhouette	logical | Whether to color the borders of the boxplots instead of the inside area.
use_test	logical | Whether to apply a statistical test to a given pair of elements. Can not be used alongside split.by.
comparisons	A list of length-2 vectors. The entries in the vector are either the names of 2 values on the x-axis or the 2 integers that correspond to the index of the columns of interest.
test	the name of the statistical test that is applied to the values of the 2 columns (e.g. t.test, wilcox.test etc.). If you implement a custom test make sure that it returns a list that has an entry called p.value.
map_signif_level	Boolean value, if the p-value are directly written as annotation or asterisks are used instead. Alternatively one can provide a named numeric vector to create custom mappings from p-values to annotation: For example: c("***"=0.001, "**"=0.01, "*"=0.05). Alternatively, one can provide a function that takes a numeric argument (the p-value) and returns a string.
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.

Value

A ggplot2 object.

Examples

  # Check Suggests.
  value <- SCpubr:::check_suggests(function_name = "do_BoxPlot", 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 box plot.
    p <- SCpubr::do_BoxPlot(sample = sample,
                            feature = "nCount_RNA")
    p

    # Use silhouette style.
    p <- SCpubr::do_BoxPlot(sample = sample,
                            feature = "nCount_RNA",
                            use_silhouette = TRUE)
    p

    # Order by mean values.
    p <- SCpubr::do_BoxPlot(sample = sample,
                            feature = "nCount_RNA",
                            order = TRUE)
    p

    # Apply second grouping.
    sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("0", "1", "2", "3"), "A", "B")
    p <- SCpubr::do_BoxPlot(sample = sample,
                            feature = "nCount_RNA",
                            split.by = "orig.ident")
    p

    # Apply statistical tests.
    p <- SCpubr::do_BoxPlot(sample = sample,
                            feature = "nCount_RNA",
                            group.by = "orig.ident",
                            use_test = TRUE,
                            comparisons = list(c("A", "B")))
    p

  } 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()`.")
  }

enblacar/SCpubr documentation built on Aug. 25, 2024, 9:45 p.m.