do_CorrelationPlot: Create correlation matrix heatmaps.

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

Create correlation matrix heatmaps.

Description

Create correlation matrix heatmaps.

Usage

do_CorrelationPlot(
  sample = NULL,
  input_gene_list = NULL,
  cluster = TRUE,
  remove.diagonal = TRUE,
  mode = "hvg",
  assay = NULL,
  group.by = NULL,
  legend.title = "Pearson coef.",
  enforce_symmetry = ifelse(mode == "hvg", TRUE, FALSE),
  font.size = 14,
  font.type = "sans",
  na.value = "grey75",
  legend.width = 1,
  legend.length = 20,
  legend.framewidth = 0.5,
  legend.tickwidth = 0.5,
  legend.framecolor = "grey50",
  legend.tickcolor = "white",
  legend.type = "colorbar",
  legend.position = "bottom",
  min.cutoff = NA,
  max.cutoff = NA,
  number.breaks = 5,
  plot.title = NULL,
  plot.subtitle = NULL,
  plot.caption = NULL,
  diverging.palette = "RdBu",
  diverging.direction = -1,
  use_viridis = FALSE,
  viridis.palette = "G",
  viridis.direction = -1,
  sequential.palette = "YlGnBu",
  sequential.direction = 1,
  axis.text.x.angle = 45,
  grid.color = "white",
  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.
input_gene_list	named_list | Named list of lists of genes to be used as input.
cluster	logical | Whether to cluster the elements in the heatmap or not.
remove.diagonal	logical | Whether to convert diagnoal to NA. Normally this value would be 1, heavily shifting the color scale.
mode	character | Different types of correlation matrices can be computed. Right now, the only possible value is "hvg", standing for Highly Variable Genes. The sample is subset for the HVG and the data is re-scaled. Scale data is used for the correlation.
assay	character | Assay to use. Defaults to the current assay.
group.by	character | Metadata variable to group the output by. Has to be a character of factor column.
legend.title	character | Title for the legend.
enforce_symmetry	logical | Return a symmetrical plot axes-wise or continuous color scale-wise, when applicable.
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.
na.value	character | Color value for NA.
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.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.
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.
plot.title, plot.subtitle, plot.caption	character | Title, subtitle or caption to use in the plot.
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.
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.
axis.text.x.angle	numeric | Degree to rotate the X labels. One of: 0, 45, 90.
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.
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.

Examples

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

    # Default values.
    p <- SCpubr::do_CorrelationPlot(sample = sample)
    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.