do_ViolinPlot: Wrapper for VlnPlot.

View source: R/do_ViolinPlot.R

do_ViolinPlotR Documentation

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.