do_DotPlot: This function is a wrapper for DotPlot. It provides most of...

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

This function is a wrapper for DotPlot. It provides most of its functionalities while adding extra. You can

Description

This function is a wrapper for DotPlot. It provides most of its functionalities while adding extra. You can

Usage

do_DotPlot(
  sample,
  features,
  assay = NULL,
  slot = "data",
  group.by = NULL,
  split.by = NULL,
  zscore.data = FALSE,
  min.cutoff = NA,
  max.cutoff = NA,
  enforce_symmetry = ifelse(base::isTRUE(zscore.data), TRUE, FALSE),
  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.nrow = NULL,
  legend.byrow = FALSE,
  dot.scale = 8,
  plot.title = NULL,
  plot.subtitle = NULL,
  plot.caption = NULL,
  xlab = NULL,
  ylab = NULL,
  font.size = 14,
  font.type = "sans",
  cluster = FALSE,
  flip = FALSE,
  axis.text.x.angle = 45,
  use_viridis = FALSE,
  viridis.palette = "G",
  viridis.direction = -1,
  sequential.palette = "YlGnBu",
  sequential.direction = 1,
  diverging.palette = "RdBu",
  diverging.direction = -1,
  na.value = "grey75",
  plot.grid = TRUE,
  grid.color = "grey75",
  grid.type = "dashed",
  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.
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.
zscore.data	logical | Whether to compute Z-scores instead of showing average expression values. This allows to see, for each gene, which group has the highest average expression, but prevents you from comparing values across genes. Can not be used with slot = "scale.data" or with split.by.
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.
enforce_symmetry	logical | Return a symmetrical plot axes-wise or continuous color scale-wise, when applicable.
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.nrow	numeric | Number of rows in the legend.
legend.byrow	logical | Whether the legend is filled by row or not.
dot.scale	numeric | Scale the size of the dots.
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.
cluster	logical | Whether to cluster the identities based on the expression of the features.
flip	logical | Whether to invert the axis of the displayed plot.
axis.text.x.angle	numeric | Degree to rotate the X labels. One of: 0, 45, 90.
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.
diverging.palette	character | Type of symmetrical color palette to use. Out of the diverging palettes defined in brewer.pal.
diverging.direction	numeric | Either 1 or -1. Direction of the divering palette. This basically flips the two ends.
na.value	character | Color value for NA.
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.
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 Dot Plot.

Examples

  # Check Suggests.
  value <- SCpubr:::check_suggests(function_name = "do_DotPlot", 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 Dot plot.
    # genes <- rownames(sample)[1:14]
    # p <- SCpubr::do_DotPlot(sample = sample,
    #                        features = genes)

  } 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.