CellStatPlot: Statistical plot of cells

In zh542370159/SCP: Single Cell Pipeline

Statistical plot of cells

Description

Statistical plot of cells

Usage

CellStatPlot(
  srt,
  stat.by,
  group.by = NULL,
  split.by = NULL,
  bg.by = NULL,
  cells = NULL,
  flip = FALSE,
  NA_color = "grey",
  NA_stat = TRUE,
  keep_empty = FALSE,
  individual = FALSE,
  stat_level = NULL,
  plot_type = c("bar", "rose", "ring", "pie", "trend", "area", "dot", "sankey", "chord",
    "venn", "upset"),
  stat_type = c("percent", "count"),
  position = c("stack", "dodge"),
  palette = "Paired",
  palcolor = NULL,
  alpha = 1,
  bg_palette = "Paired",
  bg_palcolor = NULL,
  bg_alpha = 0.2,
  label = FALSE,
  label.size = 3.5,
  label.fg = "black",
  label.bg = "white",
  label.bg.r = 0.1,
  aspect.ratio = NULL,
  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.
stat.by	The column name(s) in meta.data specifying the variable(s) to be plotted.
group.by	The column name in meta.data specifying the grouping variable.
split.by	The column name in meta.data specifying the splitting variable.
bg.by	The column name in meta.data specifying the background variable for bar plots.
cells	A character vector specifying the cells to include in the plot. Default is NULL.
flip	Logical indicating whether to flip the plot.
NA_color	The color to use for missing values.
NA_stat	Logical indicating whether to include missing values in the plot.
keep_empty	Logical indicating whether to keep empty groups in the plot.
individual	Logical indicating whether to plot individual groups separately.
stat_level	The level(s) of the variable(s) specified in stat.by to include in the plot.
plot_type	The type of plot to create. Can be one of "bar", "rose", "ring", "pie", "trend", "area", "dot", "sankey", "chord", "venn", or "upset".
stat_type	The type of statistic to compute for the plot. Can be one of "percent" or "count".
position	The position adjustment for the plot. Can be one of "stack" or "dodge".
palette	The name of the color palette to use for the plot.
palcolor	The color to use in the color palette.
alpha	The transparency level for the plot.
bg_palette	The name of the background color palette to use for bar plots.
bg_palcolor	The color to use in the background color palette.
bg_alpha	The transparency level for the background color in bar plots.
label	Logical indicating whether to add labels on the plot.
label.size	The size of the labels.
label.fg	The foreground color of the labels.
label.bg	The background color of the labels.
label.bg.r	The radius of the rounded corners of the label background.
aspect.ratio	The aspect ratio of the plot.
title	The main title of the plot.
subtitle	The subtitle of the plot.
xlab	The x-axis label of the plot.
ylab	The y-axis label of the plot.
legend.position	The position of the legend in the plot. Can be one of "right", "left", "bottom", "top", or "none".
legend.direction	The direction of the legend in the plot. Can be one of "vertical" or "horizontal".
theme_use	The name of the theme to use for the plot. Can be one of the predefined themes or a custom theme.
theme_args	A list of arguments to be passed to the theme function.
combine	Logical indicating whether to combine multiple plots into a single plot.
nrow	The number of rows in the combined plot.
ncol	The number of columns in the combined plot.
byrow	Logical indicating whether to fill the plot by row or by column.
force	Logical indicating whether to force the plot even if some variables have more than 100 levels.
seed	The random seed to use for reproducible results.

See Also

StatPlot

Examples

data("pancreas_sub")
CellStatPlot(pancreas_sub, stat.by = "Phase", group.by = "SubCellType", label = TRUE)
CellStatPlot(pancreas_sub, stat.by = "Phase", group.by = "SubCellType", label = TRUE) %>% panel_fix(height = 2, width = 3)
CellStatPlot(pancreas_sub, stat.by = "Phase", group.by = "SubCellType", stat_type = "count", position = "dodge", label = TRUE)
CellStatPlot(pancreas_sub, stat.by = "Phase", group.by = "SubCellType", bg.by = "CellType", palette = "Set1", stat_type = "count", position = "dodge")

CellStatPlot(pancreas_sub, stat.by = "Phase", plot_type = "bar")
CellStatPlot(pancreas_sub, stat.by = "Phase", plot_type = "rose")
CellStatPlot(pancreas_sub, stat.by = "Phase", plot_type = "ring")
CellStatPlot(pancreas_sub, stat.by = "Phase", plot_type = "pie")
CellStatPlot(pancreas_sub, stat.by = "Phase", plot_type = "dot")

CellStatPlot(pancreas_sub, stat.by = "Phase", group.by = "CellType", plot_type = "bar")
CellStatPlot(pancreas_sub, stat.by = "Phase", group.by = "CellType", plot_type = "rose")
CellStatPlot(pancreas_sub, stat.by = "Phase", group.by = "CellType", plot_type = "ring")
CellStatPlot(pancreas_sub, stat.by = "Phase", group.by = "CellType", plot_type = "area")
CellStatPlot(pancreas_sub, stat.by = "Phase", group.by = "CellType", plot_type = "dot")
CellStatPlot(pancreas_sub, stat.by = "Phase", group.by = "CellType", plot_type = "trend")

CellStatPlot(pancreas_sub, stat.by = "Phase", group.by = "CellType", plot_type = "bar", individual = TRUE)

CellStatPlot(pancreas_sub, stat.by = "Phase", group.by = "CellType", stat_type = "count", plot_type = "bar")
CellStatPlot(pancreas_sub, stat.by = "Phase", group.by = "CellType", stat_type = "count", plot_type = "rose")
CellStatPlot(pancreas_sub, stat.by = "Phase", group.by = "CellType", stat_type = "count", plot_type = "ring")
CellStatPlot(pancreas_sub, stat.by = "Phase", group.by = "CellType", stat_type = "count", plot_type = "area")
CellStatPlot(pancreas_sub, stat.by = "Phase", group.by = "CellType", stat_type = "count", plot_type = "dot")
CellStatPlot(pancreas_sub, stat.by = "Phase", group.by = "CellType", stat_type = "count", plot_type = "trend")

CellStatPlot(pancreas_sub, stat.by = "Phase", group.by = "CellType", stat_type = "count", plot_type = "bar", position = "dodge", label = TRUE)
CellStatPlot(pancreas_sub, stat.by = "Phase", group.by = "CellType", stat_type = "count", plot_type = "rose", position = "dodge", label = TRUE)
CellStatPlot(pancreas_sub, stat.by = "Phase", group.by = "CellType", stat_type = "count", plot_type = "ring", position = "dodge", label = TRUE)

CellStatPlot(pancreas_sub, stat.by = c("CellType", "Phase"), plot_type = "sankey")
CellStatPlot(pancreas_sub, stat.by = c("CellType", "Phase"), plot_type = "chord")

CellStatPlot(pancreas_sub,
  stat.by = c("CellType", "Phase"), plot_type = "venn",
  stat_level = list(CellType = c("Ductal", "Ngn3 low EP"), Phase = "S")
)
pancreas_sub$Progenitor <- pancreas_sub$CellType %in% c("Ngn3 low EP", "Ngn3 high EP")
pancreas_sub$G2M <- pancreas_sub$Phase == "G2M"
pancreas_sub$Sox9_Expressed <- pancreas_sub[["RNA"]]@counts["Sox9", ] > 0
pancreas_sub$Neurog3_Expressed <- pancreas_sub[["RNA"]]@counts["Neurog3", ] > 0
CellStatPlot(pancreas_sub, stat.by = c("Progenitor", "G2M", "Sox9_Expressed", "Neurog3_Expressed"), plot_type = "venn", stat_level = "TRUE")
CellStatPlot(pancreas_sub, stat.by = c("Progenitor", "G2M", "Sox9_Expressed", "Neurog3_Expressed"), plot_type = "upset", stat_level = "TRUE")
sum(pancreas_sub$Progenitor == "FALSE" &
  pancreas_sub$G2M == "FALSE" &
  pancreas_sub$Sox9_Expressed == "TRUE" &
  pancreas_sub$Neurog3_Expressed == "FALSE")

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