PAGA plot

This function generates a PAGA plot based on the given Seurat object and PAGA result.

Usage

PAGAPlot(
  srt,
  paga = srt@misc$paga,
  type = "connectivities",
  reduction = NULL,
  dims = c(1, 2),
  cells = NULL,
  show_transition = FALSE,
  node_palette = "Paired",
  node_palcolor = NULL,
  node_size = 4,
  node_alpha = 1,
  node_highlight = NULL,
  node_highlight_color = "red",
  label = FALSE,
  label.size = 3.5,
  label.fg = "white",
  label.bg = "black",
  label.bg.r = 0.1,
  label_insitu = FALSE,
  label_repel = FALSE,
  label_repulsion = 20,
  label_point_size = 1,
  label_point_color = "black",
  label_segment_color = "black",
  edge_threshold = 0.01,
  edge_line = c("straight", "curved"),
  edge_line_curvature = 0.3,
  edge_line_angle = 90,
  edge_size = c(0.2, 1),
  edge_color = "grey40",
  edge_alpha = 0.5,
  edge_shorten = 0,
  edge_offset = 0,
  edge_highlight = NULL,
  edge_highlight_color = "red",
  transition_threshold = 0.01,
  transition_line = c("straight", "curved"),
  transition_line_curvature = 0.3,
  transition_line_angle = 90,
  transition_size = c(0.2, 1),
  transition_color = "black",
  transition_alpha = 1,
  transition_arrow_type = "closed",
  transition_arrow_angle = 20,
  transition_arrow_length = grid::unit(0.02, "npc"),
  transition_shorten = 0.05,
  transition_offset = 0,
  transition_highlight = NULL,
  transition_highlight_color = "red",
  aspect.ratio = 1,
  title = "PAGA",
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  theme_use = "theme_scop",
  theme_args = list(),
  return_layer = FALSE
)

Arguments

srt: A Seurat object containing a PAGA result.
paga: The PAGA result from the Seurat object. Default is srt@misc$paga.
type: The type of plot to generate. Possible values are "connectivities" (default) and "connectivities_tree".
reduction: The type of reduction to use for the plot. Default is the default reduction in the Seurat object.
dims: The dimensions of the reduction to use for the plot. Default is the first two dimensions.
cells: The cells to include in the plot. Default is all cells.
show_transition: Whether to display transitions between different cell states. Default is FALSE.
node_palette: The color palette to use for node coloring. Default is "Paired".
node_palcolor: A vector of colors to use for node coloring. Default is NULL.
node_size: The size of the nodes in the plot. Default is 4.
node_alpha: A numeric value or column name of node specifying the transparency of the nodes.
node_highlight: A character vector specifying the names of nodes to highlight.
node_highlight_color: A character vector specifying the color for highlighting nodes.
label: Whether to show labels for the nodes.
label.size: The size of the labels.
label.fg: A character vector specifying the foreground color of the labels.
label.bg: A character vector specifying the background color of the labels.
label.bg.r: The background color transparency of the labels.
label_insitu: Whether to display the node group labels in situ or as numeric values.
label_repel: Whether to use force-directed label repulsion.
label_repulsion: The repulsion force for labels.
label_point_size: The size of the points in the labels. Default is 1.
label_point_color: The color of the points in the labels. Default is "black".
label_segment_color: The color of the lines connecting the points in the labels. Default is "black".
edge_threshold: The threshold for including edges in the plot. Default is 0.01.
edge_line: The type of line to use for the edges. Possible values are "straight" and "curved". Default is "straight".
edge_line_curvature: The curvature factor for curved edges. Default is 0.3.
edge_line_angle: The angle for curved edges. Default is 90.
edge_size: The size range for the edges. Default is c(0.2, 1).
edge_color: The color of the edges. Default is "grey40".
edge_alpha: The transparency of the edges. Default is 0.5.
edge_shorten: The amount to shorten the edges. Default is 0.
edge_offset: The offset for curved edges. Default is 0.
edge_highlight: The group(s) to highlight in the plot. Default is NULL.
edge_highlight_color: The color to use for highlighting the edges. Default is "red".
transition_threshold: The threshold for removing transitions.
transition_line: A character vector specifying the type of line for transitions (straight, curved).
transition_line_curvature: The curvature of curved transitions.
transition_line_angle: The angle of curved transitions.
transition_size: A numeric vector specifying the range of transition sizes.
transition_color: A character vector specifying the color of the transitions.
transition_alpha: The transparency of the transitions.
transition_arrow_type: A character vector specifying the type of arrow for transitions (closed, open).
transition_arrow_angle: The angle of the transition arrow.
transition_arrow_length: The length of the transition arrow.
transition_shorten: The length of the transition shorten.
transition_offset: The length of the transition offset.
transition_highlight: A character vector specifying the names of transitions to highlight.
transition_highlight_color: A character vector specifying the color for highlighting transitions.
aspect.ratio: The aspect ratio of the plot. Default is 1.
title: The title of the plot. Default is "PAGA".
subtitle: The subtitle of the plot. Default is NULL.
xlab: The label for the x-axis. Default is NULL.
ylab: The label for the y-axis. Default is NULL.
legend.position: The position of the legend. Possible values are "right", "left", "bottom", and "top". Default is "right".
legend.direction: The direction of the legend. Possible values are "vertical" and "horizontal". Default is "vertical".
theme_use: The name of the theme to use for the plot. Default is "theme_scop".
theme_args: A list of arguments to pass to the theme function. Default is list().
return_layer: Whether to return the plot as a ggplot2 layer. Default is FALSE.

Examples

if (FALSE) { # \dontrun{
data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
pancreas_sub <- RunPAGA(
  pancreas_sub,
  group_by = "SubCellType",
  linear_reduction = "PCA",
  nonlinear_reduction = "UMAP",
  return_seurat = TRUE
)

PAGAPlot(pancreas_sub)

PAGAPlot(
  pancreas_sub,
  type = "connectivities_tree"
)

PAGAPlot(
  pancreas_sub,
  reduction = "PCA"
)

PAGAPlot(
  pancreas_sub,
  reduction = "PAGAUMAP2D"
)

PAGAPlot(
  pancreas_sub,
  edge_shorten = 0.05
)

PAGAPlot(
  pancreas_sub,
  label = TRUE
)

PAGAPlot(
  pancreas_sub,
  label = TRUE,
  label_insitu = TRUE
)

PAGAPlot(
  pancreas_sub,
  label = TRUE,
  label_insitu = TRUE,
  label_repel = TRUE
)

PAGAPlot(
  pancreas_sub,
  edge_line = "curved"
)

PAGAPlot(
  pancreas_sub,
  node_size = "GroupSize"
)

PAGAPlot(
  pancreas_sub,
  node_highlight = "Ductal"
)

PAGAPlot(
  pancreas_sub,
  edge_highlight = paste(
    "Pre-endocrine",
    levels(pancreas_sub$SubCellType),
    sep = "-"
  )
)

pancreas_sub <- RunSCVELO(
  pancreas_sub,
  group_by = "SubCellType",
  linear_reduction = "PCA",
  nonlinear_reduction = "UMAP",
  return_seurat = TRUE
)

PAGAPlot(
  pancreas_sub,
  show_transition = TRUE
)

PAGAPlot(
  pancreas_sub,
  show_transition = TRUE,
  transition_offset = 0.02
)
} # }

Usage

Arguments

See also

Examples