do_GroupwiseDEPlot: Compute a dotplot with the results of a group-wise DE...

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

Compute a dotplot with the results of a group-wise DE analysis.

Description

Compute a dotplot with the results of a group-wise DE analysis.

Usage

do_GroupwiseDEPlot(
  sample,
  de_genes,
  group.by = NULL,
  assay = NULL,
  slot = "data",
  number.breaks = 5,
  dot.scale = 8,
  top_genes = 5,
  p.cutoff = 0.05,
  flip = FALSE,
  plot.title = NULL,
  plot.subtitle = NULL,
  plot.caption = NULL,
  xlab = NULL,
  ylab = NULL,
  use_viridis = FALSE,
  colors.use = NULL,
  viridis.direction = -1,
  viridis.palette = "G",
  sequential.direction = 1,
  sequential.palette = "YlGnBu",
  diverging.palette = "RdBu",
  diverging.direction = -1,
  legend.position = "bottom",
  legend.title = NULL,
  legend.width = 1,
  legend.length = 7.5,
  legend.framewidth = 0.5,
  legend.tickwidth = 0.5,
  legend.framecolor = "grey50",
  legend.tickcolor = "white",
  legend.ncol = NULL,
  legend.nrow = NULL,
  legend.byrow = FALSE,
  legend.type = "colorbar",
  font.size = 14,
  font.type = "sans",
  axis.text.x.angle = 45,
  min.cutoff = NA,
  max.cutoff = NA,
  enforce_symmetry = FALSE,
  na.value = "grey75",
  border.color = "black",
  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.
de_genes	tibble | DE genes matrix resulting of running Seurat::FindAllMarkers().
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.
slot	character | Data slot to use. Only one of: counts, data, scale.data. Defaults to "data".
number.breaks	numeric | Controls the number of breaks in continuous color scales of ggplot2-based plots.
dot.scale	numeric | Scale the size of the dots.
top_genes	numeric | Top N differentially expressed (DE) genes by group to retrieve.
p.cutoff	numeric | Cutoff to use for adjusted p.value to filter significant genes.
flip	logical | Whether to invert the axis of the displayed plot.
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.
use_viridis	logical | Whether to use viridis color scales.
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.
viridis.direction	numeric | Either 1 or -1. Controls how the gradient of viridis scale is formed.
viridis.palette	character | A capital letter from A to H or the scale name as in scale_fill_viridis.
sequential.direction	numeric | Direction of the sequential color scale. Either 1 or -1.
sequential.palette	character | Type of sequential color palette to use. Out of the sequential palettes defined in brewer.pal.
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.
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.title	character | Title for the legend.
legend.length, legend.width	numeric | Length and width of the legend. Will adjust automatically depending on legend side.
legend.framewidth, legend.tickwidth	numeric | Width of the lines of the box in the legend.
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.
legend.type	character | Type of legend to display. One of: normal: Default legend displayed by ggplot2. colorbar: Redefined colorbar legend, using guide_colorbar.
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.
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.
na.value	character | Color value for NA.
border.color	character | Color for the border of the heatmap body.
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 dotplot composed of 3 main panels: -log10(adjusted p-value), log2(FC) and mean expression by cluster.

Examples

  # Check Suggests.
  value <- SCpubr:::check_suggests(function_name = "do_GroupwiseDEPlot", 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"))

    # Compute DE genes and transform to a tibble.
    de_genes <- readRDS(system.file("extdata/de_genes_example.rds", package = "SCpubr"))

    # Default output.
    p <- SCpubr::do_GroupwiseDEPlot(sample = sample,
                                    de_genes = de_genes)

    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.