CellDimPlot: Visualize cell groups on a 2-dimensional reduction plot

In zh542370159/SCP: Single Cell Pipeline

Visualize cell groups on a 2-dimensional reduction plot

Description

Plotting cell points on a reduced 2D plane and coloring according to the groups.

Usage

CellDimPlot(
  srt,
  group.by,
  reduction = NULL,
  dims = c(1, 2),
  split.by = NULL,
  cells = NULL,
  show_na = FALSE,
  show_stat = ifelse(identical(theme_use, "theme_blank"), FALSE, TRUE),
  pt.size = NULL,
  pt.alpha = 1,
  palette = "Paired",
  palcolor = NULL,
  bg_color = "grey80",
  label = FALSE,
  label.size = 4,
  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",
  cells.highlight = NULL,
  cols.highlight = "black",
  sizes.highlight = 1,
  alpha.highlight = 1,
  stroke.highlight = 0.5,
  add_density = FALSE,
  density_color = "grey80",
  density_filled = FALSE,
  density_filled_palette = "Greys",
  density_filled_palcolor = NULL,
  add_mark = FALSE,
  mark_type = c("hull", "ellipse", "rect", "circle"),
  mark_expand = unit(3, "mm"),
  mark_alpha = 0.1,
  mark_linetype = 1,
  lineages = NULL,
  lineages_trim = c(0.01, 0.99),
  lineages_span = 0.75,
  lineages_palette = "Dark2",
  lineages_palcolor = NULL,
  lineages_arrow = arrow(length = unit(0.1, "inches")),
  lineages_linewidth = 1,
  lineages_line_bg = "white",
  lineages_line_bg_stroke = 0.5,
  lineages_whiskers = FALSE,
  lineages_whiskers_linewidth = 0.5,
  lineages_whiskers_alpha = 0.5,
  stat.by = NULL,
  stat_type = "percent",
  stat_plot_type = "pie",
  stat_plot_position = c("stack", "dodge"),
  stat_plot_size = 0.15,
  stat_plot_palette = "Set1",
  stat_palcolor = NULL,
  stat_plot_alpha = 1,
  stat_plot_label = FALSE,
  stat_plot_label_size = 3,
  graph = NULL,
  edge_size = c(0.05, 0.5),
  edge_alpha = 0.1,
  edge_color = "grey40",
  paga = NULL,
  paga_type = "connectivities",
  paga_node_size = 4,
  paga_edge_threshold = 0.01,
  paga_edge_size = c(0.2, 1),
  paga_edge_color = "grey40",
  paga_edge_alpha = 0.5,
  paga_transition_threshold = 0.01,
  paga_transition_size = c(0.2, 1),
  paga_transition_color = "black",
  paga_transition_alpha = 1,
  paga_show_transition = FALSE,
  velocity = NULL,
  velocity_plot_type = "raw",
  velocity_n_neighbors = ceiling(ncol(srt@assays[[1]])/50),
  velocity_density = 1,
  velocity_smooth = 0.5,
  velocity_scale = 1,
  velocity_min_mass = 1,
  velocity_cutoff_perc = 5,
  velocity_arrow_color = "black",
  velocity_arrow_angle = 20,
  streamline_L = 5,
  streamline_minL = 1,
  streamline_res = 1,
  streamline_n = 15,
  streamline_width = c(0, 0.8),
  streamline_alpha = 1,
  streamline_color = NULL,
  streamline_palette = "RdYlBu",
  streamline_palcolor = NULL,
  streamline_bg_color = "white",
  streamline_bg_stroke = 0.5,
  hex = FALSE,
  hex.linewidth = 0.5,
  hex.count = TRUE,
  hex.bins = 50,
  hex.binwidth = NULL,
  raster = NULL,
  raster.dpi = c(512, 512),
  aspect.ratio = 1,
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  theme_use = "theme_scp",
  theme_args = list(),
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  force = FALSE,
  seed = 11
)

Arguments

srt	A Seurat object.
group.by	Name of one or more meta.data columns to group (color) cells by (for example, orig.ident).
reduction	Which dimensionality reduction to use. If not specified, will use the reduction returned by DefaultReduction.
dims	Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions
split.by	Name of a column in meta.data column to split plot by.
cells	Subset cells to plot.
show_na	Whether to assign a color from the color palette to NA group. If FALSE, cell points with NA level will colored by bg_color.
show_stat	Whether to show statistical information on the plot.
pt.size	Point size.
pt.alpha	Point transparency.
palette	Name of a color palette name collected in SCP. Default is "Paired".
palcolor	Custom colors used to create a color palette.
bg_color	Color value for background(NA) points.
label	Whether to label the cell groups.
label.size	Size of labels.
label.fg	Foreground color of label.
label.bg	Background color of label.
label.bg.r	Background ratio of label.
label_insitu	Whether to place the raw labels (group names) in the center of the cells with the corresponding group. Default is FALSE, which using numbers instead of raw labels.
label_repel	Logical value indicating whether the label is repel away from the center points.
label_repulsion	Force of repulsion between overlapping text labels. Defaults to 20.
label_point_size	Size of the center points.
label_point_color	Color of the center points.
label_segment_color	Color of the line segment for labels.
cells.highlight	A vector of cell names to highlight.
cols.highlight	Color used to highlight the cells.
sizes.highlight	Size of highlighted cell points.
alpha.highlight	Transparency of highlighted cell points.
stroke.highlight	Border width of highlighted cell points.
add_density	Whether to add a density layer on the plot.
density_color	Color of the density contours lines.
density_filled	Whether to add filled contour bands instead of contour lines.
density_filled_palette	Color palette used to fill contour bands.
density_filled_palcolor	Custom colors used to fill contour bands.
lineages	Lineages/pseudotime to add to the plot. If specified, curves will be fitted using loess method.
lineages_trim	Trim the leading and the trailing data in the lineages.
lineages_span	The parameter α which controls the degree of smoothing in loess method.
lineages_palette	Color palette used for lineages.
lineages_palcolor	Custom colors used for lineages.
lineages_arrow	Set arrows of the lineages. See arrow.
lineages_linewidth	Width of fitted curve lines for lineages.
lineages_line_bg	Background color of curve lines for lineages.
lineages_line_bg_stroke	Border width of curve lines background.
lineages_whiskers	Whether to add whiskers for lineages.
lineages_whiskers_linewidth	Width of whiskers for lineages.
lineages_whiskers_alpha	Transparency of whiskers for lineages.
stat.by	The name of a metadata column to stat.
stat_type	Set stat types ("percent" or "count").
stat_plot_type	Set the statistical plot type.
stat_plot_position	Position adjustment in statistical plot.
stat_plot_size	Set the statistical plot size. Defaults to 0.1
stat_plot_palette	Color palette used in statistical plot.
stat_palcolor	Custom colors used in statistical plot
stat_plot_alpha	Transparency of the statistical plot.
stat_plot_label	Whether to add labels in the statistical plot.
stat_plot_label_size	Label size in the statistical plot.
graph	Specify the graph name to add edges between cell neighbors to the plot.
edge_size	Size of edges.
edge_alpha	Transparency of edges.
edge_color	Color of edges.
paga	Specify the calculated paga results to add a PAGA graph layer to the plot.
paga_type	PAGA plot type. "connectivities" or "connectivities_tree".
paga_node_size	Size of the nodes in PAGA plot.
paga_edge_threshold	Threshold of edge connectivities in PAGA plot.
paga_edge_size	Size of edges in PAGA plot.
paga_edge_color	Color of edges in PAGA plot.
paga_edge_alpha	Transparency of edges in PAGA plot.
paga_transition_threshold	Threshold of transition edges in PAGA plot.
paga_transition_size	Size of transition edges in PAGA plot.
paga_transition_color	Color of transition edges in PAGA plot.
paga_transition_alpha	Transparency of transition edges in PAGA plot.
paga_show_transition	Whether to show transitions between edges.
velocity	Specify the calculated RNA velocity mode to add a velocity layer to the plot.
velocity_plot_type	Set the velocity plot type.
velocity_n_neighbors	Set the number of neighbors used in velocity plot.
velocity_density	Set the density value used in velocity plot.
velocity_smooth	Set the smooth value used in velocity plot.
velocity_scale	Set the scale value used in velocity plot.
velocity_min_mass	Set the min_mass value used in velocity plot.
velocity_cutoff_perc	Set the cutoff_perc value used in velocity plot.
velocity_arrow_color	Color of arrows in velocity plot.
velocity_arrow_angle	Angle of arrows in velocity plot.
streamline_L	Typical length of a streamline in x and y units
streamline_minL	Minimum length of segments to show.
streamline_res	Resolution parameter (higher numbers increases the resolution).
streamline_n	Number of points to draw.
streamline_width	Size of streamline.
streamline_alpha	Transparency of streamline.
streamline_color	Color of streamline.
streamline_palette	Color palette used for streamline.
streamline_palcolor	Custom colors used for streamline.
streamline_bg_color	Background color of streamline.
streamline_bg_stroke	Border width of streamline background.
hex	Whether to chane the plot type from point to the hexagonal bin.
hex.linewidth	Border width of hexagonal bins.
hex.count	Whether show cell counts in each hexagonal bin.
hex.bins	Number of hexagonal bins.
hex.binwidth	Hexagonal bin width.
raster	Convert points to raster format, default is NULL which automatically rasterizes if plotting more than 100,000 cells
raster.dpi	Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).
aspect.ratio	Aspect ratio of the panel.
title	The text for the title.
subtitle	The text for the subtitle for the plot which will be displayed below the title.
xlab	x-axis label.
ylab	y-axis label.
legend.position	The position of legends ("none", "left", "right", "bottom", "top").
legend.direction	Layout of items in legends ("horizontal" or "vertical")
theme_use	Theme used. Can be a character string or a theme function. For example, "theme_blank" or ggplot2::theme_classic.
theme_args	Other arguments passed to the theme_use.
combine	Combine plots into a single patchwork object. If FALSE, return a list of ggplot objects.
nrow	Number of rows in the combined plot.
ncol	Number of columns in the combined plot.
byrow	Logical value indicating if the plots should be arrange by row (default) or by column.
force	Whether to force drawing regardless of maximum levels in any cell group is greater than 100.
seed	Random seed set for reproducibility

See Also

FeatureDimPlot

Examples

data("pancreas_sub")
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP")
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", theme_use = "theme_blank")
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", theme_use = ggplot2::theme_classic, theme_args = list(base_size = 16))
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP") %>% panel_fix(height = 2, raster = TRUE, dpi = 30)

# Highlight cells
CellDimPlot(pancreas_sub,
  group.by = "SubCellType", reduction = "UMAP",
  cells.highlight = colnames(pancreas_sub)[pancreas_sub$SubCellType == "Epsilon"]
)
CellDimPlot(pancreas_sub,
  group.by = "SubCellType", split.by = "Phase", reduction = "UMAP",
  cells.highlight = TRUE, theme_use = "theme_blank", legend.position = "none"
)

# Add group labels
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", label = TRUE)
CellDimPlot(pancreas_sub,
  group.by = "SubCellType", reduction = "UMAP",
  label = TRUE, label.fg = "orange", label.bg = "red", label.size = 5
)
CellDimPlot(pancreas_sub,
  group.by = "SubCellType", reduction = "UMAP",
  label = TRUE, label_insitu = TRUE
)
CellDimPlot(pancreas_sub,
  group.by = "SubCellType", reduction = "UMAP",
  label = TRUE, label_insitu = TRUE, label_repel = TRUE, label_segment_color = "red"
)

# Add various shape of marks
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", add_mark = TRUE)
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", add_mark = TRUE, mark_expand = unit(1, "mm"))
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", add_mark = TRUE, mark_alpha = 0.3)
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", add_mark = TRUE, mark_linetype = 2)
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", add_mark = TRUE, mark_type = "ellipse")
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", add_mark = TRUE, mark_type = "rect")
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", add_mark = TRUE, mark_type = "circle")

# Add a density layer
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", add_density = TRUE)
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", add_density = TRUE, density_filled = TRUE)
CellDimPlot(pancreas_sub,
  group.by = "SubCellType", reduction = "UMAP",
  add_density = TRUE, density_filled = TRUE, density_filled_palette = "Blues",
  cells.highlight = TRUE
)

# Add statistical charts
CellDimPlot(pancreas_sub, group.by = "CellType", reduction = "UMAP", stat.by = "Phase")
CellDimPlot(pancreas_sub, group.by = "CellType", reduction = "UMAP", stat.by = "Phase", stat_plot_type = "ring", stat_plot_label = TRUE, stat_plot_size = 0.15)
CellDimPlot(pancreas_sub, group.by = "CellType", reduction = "UMAP", stat.by = "Phase", stat_plot_type = "bar", stat_type = "count", stat_plot_position = "dodge")

# Chane the plot type from point to the hexagonal bin
CellDimPlot(pancreas_sub, group.by = "CellType", reduction = "UMAP", hex = TRUE)
CellDimPlot(pancreas_sub, group.by = "CellType", reduction = "UMAP", hex = TRUE, hex.bins = 20)
CellDimPlot(pancreas_sub, group.by = "CellType", reduction = "UMAP", hex = TRUE, hex.count = FALSE)

# Show neighbors graphs on the plot
pancreas_sub <- Standard_SCP(pancreas_sub)
CellDimPlot(pancreas_sub, group.by = "CellType", reduction = "UMAP", graph = "Standardpca_SNN")
CellDimPlot(pancreas_sub, group.by = "CellType", reduction = "UMAP", graph = "Standardpca_SNN", edge_color = "grey80")

# Show lineages on the plot based on the pseudotime
pancreas_sub <- RunSlingshot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", show_plot = FALSE)
FeatureDimPlot(pancreas_sub, features = paste0("Lineage", 1:3), reduction = "UMAP")
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", lineages = paste0("Lineage", 1:3))
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", lineages = paste0("Lineage", 1:3), lineages_whiskers = TRUE)
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", lineages = paste0("Lineage", 1:3), lineages_span = 0.1)

# Show PAGA results on the plot
pancreas_sub <- RunPAGA(srt = pancreas_sub, group_by = "SubCellType", linear_reduction = "PCA", nonlinear_reduction = "UMAP", return_seurat = TRUE)
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", paga = pancreas_sub@misc$paga)
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", paga = pancreas_sub@misc$paga, paga_type = "connectivities_tree")
CellDimPlot(pancreas_sub,
  group.by = "SubCellType", reduction = "UMAP", pt.size = 5, pt.alpha = 0.2,
  label = TRUE, label_repel = TRUE, label_insitu = TRUE, label_segment_color = "transparent",
  paga = pancreas_sub@misc$paga, paga_edge_threshold = 0.1, paga_edge_color = "black", paga_edge_alpha = 1,
  legend.position = "none", theme_use = "theme_blank"
)

# Show RNA velocity results on the plot
pancreas_sub <- RunSCVELO(srt = pancreas_sub, group_by = "SubCellType", linear_reduction = "PCA", nonlinear_reduction = "UMAP", mode = "stochastic", return_seurat = TRUE)
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", paga = pancreas_sub@misc$paga, paga_show_transition = TRUE)
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", pt.size = NA, velocity = "stochastic")
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", pt.size = 5, pt.alpha = 0.2, velocity = "stochastic", velocity_plot_type = "grid")
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", pt.size = 5, pt.alpha = 0.2, velocity = "stochastic", velocity_plot_type = "grid", velocity_scale = 1.5)
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", pt.size = 5, pt.alpha = 0.2, velocity = "stochastic", velocity_plot_type = "stream")
CellDimPlot(pancreas_sub,
  group.by = "SubCellType", reduction = "UMAP", pt.size = 5, pt.alpha = 0.2,
  label = TRUE, label_insitu = TRUE,
  velocity = "stochastic", velocity_plot_type = "stream", velocity_arrow_color = "yellow",
  velocity_density = 2, velocity_smooth = 1, streamline_n = 20, streamline_color = "black",
  legend.position = "none", theme_use = "theme_blank"
)

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