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)
#> Error in check_Python("scanpy"): could not find function "check_Python"
PAGAPlot(pancreas_sub)
#> Error in PAGAPlot(pancreas_sub): Cannot find the paga result.
PAGAPlot(pancreas_sub, type = "connectivities_tree")
#> Error in PAGAPlot(pancreas_sub, type = "connectivities_tree"): Cannot find the paga result.
PAGAPlot(pancreas_sub, reduction = "PCA")
#> Error in PAGAPlot(pancreas_sub, reduction = "PCA"): Cannot find the paga result.
PAGAPlot(pancreas_sub, reduction = "PAGAUMAP2D")
#> Error in PAGAPlot(pancreas_sub, reduction = "PAGAUMAP2D"): Cannot find the paga result.
PAGAPlot(pancreas_sub, edge_shorten = 0.05)
#> Error in PAGAPlot(pancreas_sub, edge_shorten = 0.05): Cannot find the paga result.
PAGAPlot(pancreas_sub, label = TRUE)
#> Error in PAGAPlot(pancreas_sub, label = TRUE): Cannot find the paga result.
PAGAPlot(pancreas_sub, label = TRUE, label_insitu = TRUE)
#> Error in PAGAPlot(pancreas_sub, label = TRUE, label_insitu = TRUE): Cannot find the paga result.
PAGAPlot(pancreas_sub, label = TRUE, label_insitu = TRUE, label_repel = TRUE)
#> Error in PAGAPlot(pancreas_sub, label = TRUE, label_insitu = TRUE, label_repel = TRUE): Cannot find the paga result.
PAGAPlot(pancreas_sub, edge_line = "curved")
#> Error in PAGAPlot(pancreas_sub, edge_line = "curved"): Cannot find the paga result.
PAGAPlot(pancreas_sub, node_size = "GroupSize")
#> Error in PAGAPlot(pancreas_sub, node_size = "GroupSize"): Cannot find the paga result.
PAGAPlot(pancreas_sub, node_highlight = "Ductal")
#> Error in PAGAPlot(pancreas_sub, node_highlight = "Ductal"): Cannot find the paga result.
PAGAPlot(pancreas_sub, edge_highlight = paste("Pre-endocrine", levels(pancreas_sub$SubCellType), sep = "-"))
#> Error in PAGAPlot(pancreas_sub, edge_highlight = paste("Pre-endocrine", levels(pancreas_sub$SubCellType), sep = "-")): Cannot find the paga result.
pancreas_sub <- RunSCVELO(srt = pancreas_sub, group_by = "SubCellType", linear_reduction = "PCA", nonlinear_reduction = "UMAP", return_seurat = TRUE)
#> Python module 'scvelo' is required for velocity analysis but is not installed.
#> To install, run: PrepareEnv() and then check_Python('scvelo')
#> Error in RunSCVELO(srt = pancreas_sub, group_by = "SubCellType", linear_reduction = "PCA", nonlinear_reduction = "UMAP", return_seurat = TRUE): Required Python module 'scvelo' is not available. Please install it first.
PAGAPlot(pancreas_sub, show_transition = TRUE)
#> Error in PAGAPlot(pancreas_sub, show_transition = TRUE): Cannot find the paga result.
PAGAPlot(pancreas_sub, show_transition = TRUE, transition_offset = 0.02)
#> Error in PAGAPlot(pancreas_sub, show_transition = TRUE, transition_offset = 0.02): Cannot find the paga result.