do_ViolinPlot: Wrapper for VlnPlot.

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

Wrapper for VlnPlot.

Description

Wrapper for VlnPlot.

Usage

do_ViolinPlot(
  sample,
  features,
  assay = NULL,
  slot = NULL,
  group.by = NULL,
  split.by = NULL,
  colors.use = NULL,
  pt.size = 0,
  line_width = 0.5,
  y_cut = rep(NA, length(features)),
  plot_boxplot = TRUE,
  boxplot_width = 0.2,
  legend.position = "bottom",
  plot.title = NULL,
  plot.subtitle = NULL,
  plot.caption = NULL,
  xlab = rep(NA, length(features)),
  ylab = rep(NA, length(features)),
  font.size = 14,
  font.type = "sans",
  axis.text.x.angle = 45,
  plot.grid = TRUE,
  grid.color = "grey75",
  grid.type = "dashed",
  order = TRUE,
  flip = FALSE,
  ncol = NULL,
  share.y.lims = FALSE,
  legend.title = NULL,
  legend.title.position = "top",
  legend.ncol = NULL,
  legend.nrow = NULL,
  legend.byrow = FALSE,
  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.
features	character | Features to represent.
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".
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.
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.
pt.size	numeric | Size of points in the Violin plot.
line_width	numeric | Width of the lines drawn in the plot. Defaults to 1.
y_cut	numeric | Vector with the values in which the Violins should be cut. Only works for one feature.
plot_boxplot	logical | Whether to plot a Box plot inside the violin or not.
boxplot_width	numeric | Width of the boxplots. Defaults to 0.2.
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.
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.
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.
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.
order	logical | Whether to order the boxplots by average values. Can not be used alongside split.by.
flip	logical | Whether to invert the axis of the displayed plot.
ncol	numeric | Number of columns used in the arrangement of the output plot using "split.by" parameter.
share.y.lims	logical | When querying multiple features, force the Y axis of all of them to be on the same range of values (this being the max and min of all features combined).
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.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.
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 containing a Violin Plot.

Examples

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

    # Remove the box plots.
    p <- SCpubr::do_ViolinPlot(sample = sample,
                               feature = "nCount_RNA",
                               plot_boxplot = FALSE)
    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.