do_LigandReceptorPlot: Visualize Ligand-Receptor analysis output.

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

Visualize Ligand-Receptor analysis output.

Description

This function makes use of liana package to run Ligand-Receptor analysis. Takes the output of liana and generates a dot-plot visualization according to the user's specifications.

Usage

do_LigandReceptorPlot(
  liana_output,
  split.by = NULL,
  keep_source = NULL,
  keep_target = NULL,
  top_interactions = 25,
  top_interactions_by_group = FALSE,
  dot_border = TRUE,
  magnitude = "sca.LRscore",
  specificity = "aggregate_rank",
  sort.by = "E",
  sorting.type.specificity = "descending",
  sorting.type.magnitude = "descending",
  border.color = "black",
  axis.text.x.angle = 45,
  legend.position = "bottom",
  legend.type = "colorbar",
  legend.length = 20,
  legend.width = 1,
  legend.framecolor = "grey50",
  legend.tickcolor = "white",
  legend.framewidth = 0.5,
  legend.tickwidth = 0.5,
  use_viridis = FALSE,
  viridis.palette = "G",
  viridis.direction = 1,
  sequential.palette = "YlGnBu",
  sequential.direction = 1,
  font.size = 14,
  dot.size = 1,
  font.type = "sans",
  plot.grid = TRUE,
  grid.color = "grey90",
  grid.type = "dotted",
  compute_ChordDiagrams = FALSE,
  sort_interactions_alphabetically = FALSE,
  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",
  return_interactions = FALSE,
  invert_specificity = TRUE,
  invert_magnitude = FALSE,
  verbose = TRUE
)

Arguments

liana_output	tibble | Object resulting from running liana_wrap and liana_aggregate.
split.by	character | Whether to further facet the plot on the y axis by common ligand.complex or receptor.complex. Values to provide: NULL, ligand.complex, receptor.complex.
keep_source, keep_target	character | Identities to keep for the source/target of the interactions. NULL otherwise.
top_interactions	numeric | Number of unique interactions to retrieve ordered by magnitude and specificity. It does not necessarily mean that the output will contain as many, but rather an approximate value.
top_interactions_by_group	logical | Enforce the value on top_interactions to be applied to each group in source column.
dot_border	logical | Whether to draw a black border in the dots.
specificity, magnitude	character | Which columns to use for specificity and magnitude.
sort.by	character | How to arrange the top interactions. Interactions are sorted and then the top N are retrieved and displayed. This takes place after subsetting for keep_source and keep_target One of: A: Sorts by specificity. B: Sorts by magnitude. C: Sorts by specificity, then magnitude (gives extra weight to specificity). D: Sorts by magnitude, then specificity (gives extra weight to magnitude). Might lead to the display of non-significant results. E: Sorts by specificity and magnitude equally.
sorting.type.specificity, sorting.type.magnitude	character | Whether the sorting of e magnitude or specificity columns is done in ascending or descending order. This synergises with the value of e invert_specificity and e invert_magnitude parameters.
border.color	character | Color for the border of the heatmap body.
axis.text.x.angle	numeric | Degree to rotate the X labels. One of: 0, 45, 90.
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.type	character | Type of legend to display. One of: normal: Default legend displayed by ggplot2. colorbar: Redefined colorbar legend, using guide_colorbar.
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.framewidth, legend.tickwidth	numeric | Width of the lines of the box in the legend.
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.
font.size	numeric | Overall font size of the plot. All plot elements will have a size relationship with this font size.
dot.size	numeric | Size aesthetic for 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.
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.
compute_ChordDiagrams	logical | Whether to also compute Chord Diagrams for both the number of interactions between source and target but also between ligand.complex and receptor.complex.
sort_interactions_alphabetically	logical | Sort the interactions to be plotted alphabetically (TRUE) or keep them in their original order in the matrix (FALSE).
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.
return_interactions	logical | Whether to return the data.frames with the interactions so that they can be plotted as chord plots using other package functions.
invert_specificity, invert_magnitude	logical | Whether to -log10 transform specificity and magnitude columns.
verbose	logical | Whether to show extra comments, warnings,etc.

Value

A ggplot2 plot with the results of the Ligand-Receptor analysis.

Examples

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

  if (isTRUE(value)){
    liana_output <- readRDS(system.file("extdata/liana_output_example.rds", package = "SCpubr"))
    # Ligand Receptor analysis plot.
    p <- SCpubr::do_LigandReceptorPlot(liana_output = liana_output)
    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.