PAGAPlot: PAGA plot
In zh542370159/SCP: Single Cell Pipeline

PAGAPlot

R Documentation

PAGA plot

Description

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 = 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_scp",
  theme_args = list(),
  return_layer = FALSE
)

Arguments

`srt`	A Seurat object containing a PAGA result.
`paga`	The PAGA result from the Seurat object. Defaults to `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. Defaults to the default reduction in the Seurat object.
`dims`	The dimensions of the reduction to use for the plot. Defaults to the first two dimensions.
`cells`	The cells to include in the plot. Defaults to all cells.
`show_transition`	A logical value indicating whether to display transitions between different cell states. Defaults to `FALSE`.
`node_palette`	The color palette to use for node coloring. Defaults to "Paired".
`node_palcolor`	A vector of colors to use for node coloring. Defaults to `NULL`.
`node_size`	The size of the nodes in the plot. Defaults to 4.
`node_alpha`	The transparency of the nodes in the plot. Defaults to 1.
`node_highlight`	The group(s) to highlight in the plot. Defaults to `NULL`.
`node_highlight_color`	The color to use for highlighting the nodes. Defaults to "red".
`label`	A logical value indicating whether to display labels for the nodes. Defaults to `FALSE`.
`label.size`	The size of the labels. Defaults to 3.5.
`label.fg`	The color of the label text. Defaults to "white".
`label.bg`	The background color of the labels. Defaults to "black".
`label.bg.r`	The transparency of the label background color. Defaults to 0.1.
`label_insitu`	A logical value indicating whether to use in-situ labeling for the nodes. Defaults to `FALSE`.
`label_repel`	A logical value indicating whether to use repel mode for labeling nodes. Defaults to `FALSE`.
`label_repulsion`	The repulsion factor for repel mode. Defaults to 20.
`label_point_size`	The size of the points in the labels. Defaults to 1.
`label_point_color`	The color of the points in the labels. Defaults to "black".
`label_segment_color`	The color of the lines connecting the points in the labels. Defaults to "black".
`edge_threshold`	The threshold for including edges in the plot. Defaults to 0.01.
`edge_line`	The type of line to use for the edges. Possible values are "straight" and "curved". Defaults to "straight".
`edge_line_curvature`	The curvature factor for curved edges. Defaults to 0.3.
`edge_line_angle`	The angle for curved edges. Defaults to 90.
`edge_size`	The size range for the edges. Defaults to c(0.2, 1).
`edge_color`	The color of the edges. Defaults to "grey40".
`edge_alpha`	The transparency of the edges. Defaults to 0.5.
`edge_shorten`	The amount to shorten the edges. Defaults to 0.
`edge_offset`	The offset for curved edges. Defaults to 0.
`edge_highlight`	The group(s) to highlight in the plot. Defaults to `NULL`.
`edge_highlight_color`	The color to use for highlighting the edges. Defaults to "red".
`transition_threshold`	The threshold for including transitions in the plot. Defaults to 0.01.
`transition_line`	The type of line to use for the transitions. Possible values are "straight" and "curved". Defaults to "straight".
`transition_line_curvature`	The curvature factor for curved transitions. Defaults to 0.3.
`transition_line_angle`	The angle for curved transitions. Defaults to 90.
`transition_size`	The size range for the transitions. Defaults to c(0.2, 1).
`transition_color`	The color of the transitions. Defaults to "black".
`transition_alpha`	The transparency of the transitions. Defaults to 1.
`transition_arrow_type`	The type of arrow to use for the transitions. Possible values are "closed", "open", and "triangle". Defaults to "closed".
`transition_arrow_angle`	The angle of the arrow for transitions. Defaults to 20.
`transition_arrow_length`	The length of the arrow for transitions. Defaults to unit(0.02, "npc").
`transition_shorten`	The amount to shorten the transitions. Defaults to 0.05.
`transition_offset`	The offset for curved transitions. Defaults to 0.
`transition_highlight`	The group(s) to highlight in the plot. Defaults to `NULL`.
`transition_highlight_color`	The color to use for highlighting the transitions. Defaults to "red".
`aspect.ratio`	The aspect ratio of the plot. Defaults to 1.
`title`	The title of the plot. Defaults to "PAGA".
`subtitle`	The subtitle of the plot. Defaults to `NULL`.
`xlab`	The label for the x-axis. Defaults to `NULL`.
`ylab`	The label for the y-axis. Defaults to `NULL`.
`legend.position`	The position of the legend. Possible values are "right", "left", "bottom", and "top". Defaults to "right".
`legend.direction`	The direction of the legend. Possible values are "vertical" and "horizontal". Defaults to "vertical".
`theme_use`	The name of the theme to use for the plot. Defaults to "theme_scp".
`theme_args`	A list of arguments to pass to the theme function. Defaults to an empty list.
`return_layer`	A logical value indicating whether to return the plot as a ggplot2 layer. Defaults to `FALSE`.

Examples

data("pancreas_sub")
pancreas_sub <- RunPAGA(srt = 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(srt = 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)

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.