do_BeeSwarmPlot: BeeSwarm plot.

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

BeeSwarm plot.

Description

BeeSwarm plot.

Usage

do_BeeSwarmPlot(
  sample,
  feature_to_rank,
  group.by = NULL,
  assay = NULL,
  reduction = NULL,
  slot = NULL,
  continuous_feature = FALSE,
  order = FALSE,
  colors.use = NULL,
  legend.title = NULL,
  legend.type = "colorbar",
  legend.position = "bottom",
  legend.framewidth = 0.5,
  legend.tickwidth = 0.5,
  legend.length = 20,
  legend.width = 1,
  legend.framecolor = "grey50",
  legend.tickcolor = "white",
  legend.ncol = NULL,
  legend.icon.size = 4,
  plot.title = NULL,
  plot.subtitle = NULL,
  plot.caption = NULL,
  xlab = NULL,
  ylab = NULL,
  font.size = 14,
  font.type = "sans",
  remove_x_axis = FALSE,
  remove_y_axis = FALSE,
  flip = FALSE,
  use_viridis = FALSE,
  viridis.palette = "G",
  viridis.direction = 1,
  sequential.palette = "YlGnBu",
  sequential.direction = 1,
  verbose = TRUE,
  raster = FALSE,
  raster.dpi = 300,
  plot_cell_borders = TRUE,
  border.size = 1.5,
  border.color = "black",
  pt.size = 2,
  min.cutoff = NA,
  max.cutoff = NA,
  na.value = "grey75",
  number.breaks = 5,
  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_to_rank	character | Feature for which the cells are going to be ranked. Ideal case is that this feature is stored as a metadata column.
group.by	character | Metadata variable to group the output by. Has to be a character of factor column.
assay	character | Assay to use. Defaults to the current assay.
reduction	character | Reduction to use. Can be the canonical ones such as "umap", "pca", or any custom ones, such as "diffusion". If you are unsure about which reductions you have, use Seurat::Reductions(sample). Defaults to "umap" if present or to the last computed reduction if the argument is not provided.
slot	character | Data slot to use. Only one of: counts, data, scale.data. Defaults to "data".
continuous_feature	logical | Is the feature to rank and color for continuous? I.e: an enrichment score.
order	logical | Whether to reorder the groups based on the median of the ranking.
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.
legend.title	character | Title for the legend.
legend.type	character | Type of legend to display. One of: normal: Default legend displayed by ggplot2. colorbar: Redefined colorbar legend, using guide_colorbar.
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.framewidth, legend.tickwidth	numeric | Width of the lines of the box in the legend.
legend.length, legend.width	numeric | Length and width of the legend. Will adjust automatically depending on legend side.
legend.framecolor	character | Color of the lines of the box in the legend.
legend.tickcolor	character | Color of the ticks of the box in the legend.
legend.ncol	numeric | Number of columns in the legend.
legend.icon.size	numeric | Size of the icons in legend.
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.
remove_x_axis, remove_y_axis	logical | Remove X axis labels and ticks from the plot.
flip	logical | Whether to invert the axis of the displayed plot.
use_viridis	logical | Whether to use viridis color scales.
viridis.palette	character | A capital letter from A to H or the scale name as in scale_fill_viridis.
viridis.direction	numeric | Either 1 or -1. Controls how the gradient of viridis scale is formed.
sequential.palette	character | Type of sequential color palette to use. Out of the sequential palettes defined in brewer.pal.
sequential.direction	numeric | Direction of the sequential color scale. Either 1 or -1.
verbose	logical | Whether to show extra comments, warnings,etc.
raster	logical | Whether to raster the resulting plot. This is recommendable if plotting a lot of cells.
raster.dpi	numeric | Pixel resolution for rasterized plots. Defaults to 1024. Only activates on Seurat versions higher or equal than 4.1.0.
plot_cell_borders	logical | Whether to plot border around cells.
border.size	numeric | Width of the border of the cells.
border.color	character | Color for the border of the heatmap body.
pt.size	numeric | Size of the dots.
min.cutoff, max.cutoff	numeric | Set the min/max ends of the color scale. Any cell/group with a value lower than min.cutoff will turn into min.cutoff and any cell with a value higher than max.cutoff will turn into max.cutoff. In FeaturePlots, provide as many values as features. Use NAs to skip a feature.
na.value	character | Color value for NA.
number.breaks	numeric | Controls the number of breaks in continuous color scales of ggplot2-based plots.
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 Bee Swarm plot.

Examples

  # Check Suggests.
  value <- SCpubr:::check_suggests(function_name = "do_BeeSwarmPlot", 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 Bee Swarm plot - categorical coloring.
    # This will color based on the unique values of seurat_clusters.
    p <- SCpubr::do_BeeSwarmPlot(sample = sample,
                                 feature_to_rank = "PC_1",
                                 group.by = "seurat_clusters",
                                 continuous_feature = FALSE)

    # Basic Bee Swarm plot - continuous coloring.
    # This will color based on the PC_1 values.
    p <- SCpubr::do_BeeSwarmPlot(sample = sample,
                                 feature_to_rank = "PC_1",
                                 group.by = "seurat_clusters",
                                 continuous_feature = TRUE)
  } 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.