do_CNVHeatmap: Display CNV scores from inferCNV as Feature Plots.

Description

Display CNV scores from inferCNV as Feature Plots.

Usage

do_CNVHeatmap(
  sample,
  infercnv_object,
  chromosome_locations,
  group.by = NULL,
  using_metacells = FALSE,
  metacell_mapping = NULL,
  include_chr_arms = FALSE,
  values.show = FALSE,
  values.threshold = NULL,
  values.size = 3,
  values.round = 1,
  legend.type = "colorbar",
  legend.position = "bottom",
  legend.length = 20,
  legend.width = 1,
  legend.framewidth = 0.5,
  legend.tickwidth = 0.5,
  legend.framecolor = "grey50",
  legend.tickcolor = "white",
  font.size = 14,
  pt.size = 1,
  font.type = "sans",
  axis.text.x.angle = 45,
  enforce_symmetry = TRUE,
  legend.title = NULL,
  na.value = "grey75",
  viridis.palette = "G",
  viridis.direction = 1,
  verbose = FALSE,
  min.cutoff = NA,
  max.cutoff = NA,
  number.breaks = 5,
  diverging.palette = "RdBu",
  diverging.direction = -1,
  sequential.palette = "YlGnBu",
  sequential.direction = -1,
  use_viridis = TRUE,
  return_object = FALSE,
  grid.color = "white",
  border.color = "black",
  flip = 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"
)

Value

A list containing Feature Plots for different chromosome regions and corresponding dot plots by groups..

Arguments

sample

Seurat | A Seurat object, generated by CreateSeuratObject.

infercnv_object

infercnv | Output inferCNV object run on the same Seurat object.

chromosome_locations

tibble | Tibble containing the chromosome regions to use. Can be obtained using utils::data("human_chr_locations", package = "SCpubr").

group.by

character | Metadata variable to group the output by. Has to be a character of factor column.

using_metacells

logical | Whether inferCNV was run using metacells or not.

metacell_mapping

named_vector | Vector or cell - metacell mapping.

include_chr_arms

logical | Whether the output heatmap should also include chromosome arms or just whole chromosomes.

values.show

logical | Whether to add values as text in the heatmap.

values.threshold

numeric | Value from which the text color turns from black to white. If mode = "hvg", this is applied to both ends of the color scale.

values.size

numeric | Size of the text labels.

values.round

numeric | Decimal to which round the values to.

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.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.

font.size

numeric | Overall font size of the plot. All plot elements will have a size relationship with this font size.

pt.size

numeric | Size of the dots.

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.

enforce_symmetry

logical | Return a symmetrical plot axes-wise or continuous color scale-wise, when applicable.

legend.title

character | Title for the legend.

na.value

character | Color value for NA.

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.

verbose

logical | Whether to show extra comments, warnings,etc.

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.

number.breaks

numeric | Controls the number of breaks in continuous color scales of ggplot2-based plots.

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.

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.

use_viridis

logical | Whether to use viridis color scales.

return_object

logical | Returns the Seurat object with the modifications performed in the function. Nomally, this contains a new assay with the data that can then be used for any other visualization desired.

grid.color

character | Color of the grid in the plot. In heatmaps, color of the border of the cells.

border.color

character | Color for the border of the heatmap body.

flip

logical | Whether to invert the axis of the displayed plot.

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.

Examples

Run this code

# \donttest{
  # Check Suggests.
  value <- SCpubr:::check_suggests(function_name = "do_CNVHeatmap", passive = TRUE)

  if (isTRUE(value)){
    # Consult the full documentation in https://enblacar.github.io/SCpubr-book/

    # This function expects that you have run inferCNV on your
    # own and you have access to the output object.

    # Define your Seurat object.
    sample <- readRDS(system.file("extdata/seurat_dataset_example.rds",
                                  package = "SCpubr"))

    # Define your inferCNV object.
    infercnv_object <- readRDS(system.file("extdata/infercnv_object_example.rds",
                                           package = "SCpubr"))

    # Get human chromosome locations.
    chromosome_locations = SCpubr::human_chr_locations

    # Compute for a all chromosomes.
    p <- SCpubr::do_CNVHeatmap(sample = sample,
                                          infercnv_object = infercnv_object,
                                          using_metacells = FALSE,
                                          chromosome_locations = chromosome_locations)

  } 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()`.")
  }
# }

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