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Statistical plot of cells

Source: R/CellStatPlot.R
CellStatPlot.Rd

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", "trend_alluvial", "area", "dot",
    "sankey", "chord", "venn", "upset"),
  stat_type = c("percent", "count"),
  position = c("stack", "dodge"),
  palette = "Chinese",
  palcolor = NULL,
  alpha = 1,
  bg_palette = "Chinese",
  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_scop",
  theme_args = list(),
  grid_major = TRUE,
  grid_major_colour = "grey80",
  grid_major_linetype = 2,
  grid_major_linewidth = 0.3,
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  force = FALSE,
  seed = 11,
  ...
)

Arguments

srt

A Seurat object.

stat.by

A character vector specifying the features to plot.

group.by

Name of one or more meta.data columns to group (color) cells by.

split.by

Name of a column in meta.data column to split plot by. Default is NULL.

bg.by

A character vector specifying the variable to use as the background color. Default is NULL.

cells

A character vector of cell names to use. Default is NULL.

flip

A logical specifying whether to flip the plot vertically. Default is FALSE.

NA_color

The color to use for missing values.

NA_stat

Whether to include missing values in the plot. Default is TRUE.

keep_empty

Whether to keep empty levels in the plot. Default is FALSE.

individual

Whether to create individual plots for each group. Default is FALSE.

stat_level

The level(s) of the variable(s) specified in stat.by to include in the plot. Default is NULL.

plot_type

The type of plot to create. Can be one of "bar", "rose", "ring", "pie", "trend", "trend_alluvial", "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

Color palette name. Available palettes can be found in thisplot::show_palettes. Default is "Chinese".

palcolor

Custom colors used to create a color palette. Default is NULL.

alpha

The transparency of the plot. Default is 1.

bg_palette

A string specifying the color palette to use for the background. Default is "Chinese".

bg_palcolor

A character vector specifying specific colors to use for the background. Default is NULL.

bg_alpha

The transparency of the background. Default is 0.2.

label

Whether to add labels on the plot. Default is FALSE.

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

Aspect ratio of the panel. Default is NULL.

title

The text for the title. Default is NULL.

subtitle

The text for the subtitle for the plot which will be displayed below the title. Default is NULL.

xlab

The x-axis label of the plot. Default is NULL.

ylab

A string specifying the label of the y-axis. Default is "Expression level".

legend.position

The position of legends, one of "none", "left", "right", "bottom", "top". Default is "right".

legend.direction

The direction of the legend in the plot. Can be one of "vertical" or "horizontal".

theme_use

Theme used. Can be a character string or a theme function. Default is "theme_scop".

theme_args

Other arguments passed to the theme_use. Default is list().

grid_major

Whether to show major panel grid lines. Default is TRUE.

grid_major_colour

Color of major panel grid lines.

grid_major_linetype

Linetype of major panel grid lines.

grid_major_linewidth

Line width of major panel grid lines.

combine

Combine plots into a single patchwork object. If FALSE, return a list of ggplot objects.

nrow

Number of rows in the combined plot. Default is NULL, which means determined automatically based on the number of plots.

ncol

Number of columns in the combined plot. Default is NULL, which means determined automatically based on the number of plots.

byrow

Whether to arrange the plots by row in the combined plot. Default is TRUE.

force

Whether to force drawing regardless of maximum levels in any cell group is greater than 100. Default is FALSE.

seed

Random seed for reproducibility. Default is 11.

...

Additional arguments passed to the other functions.

See also

FeatureStatPlot

Examples

data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
p1 <- CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "SubCellType",
  label = TRUE
)
p1

thisplot::panel_fix(
  p1,
  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 = "trend_alluvial"
)

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$Fancb_Expressed <- GetAssayData5(
  pancreas_sub,
  assay = "RNA",
  layer = "counts"
)["Fancb", ] > 0
pancreas_sub$Dlg3_Expressed <- GetAssayData5(
  pancreas_sub,
  assay = "RNA",
  layer = "counts"
)["Dlg3", ] > 0

CellStatPlot(
  pancreas_sub,
  stat.by = c(
    "Progenitor", "G2M", "Fancb_Expressed", "Dlg3_Expressed"
  ),
  plot_type = "venn",
  stat_level = "TRUE"
)

CellStatPlot(
  pancreas_sub,
  stat.by = c(
    "Progenitor", "G2M", "Fancb_Expressed", "Dlg3_Expressed"
  ),
  plot_type = "upset",
  stat_level = "TRUE"
)

sum(
  pancreas_sub$Progenitor == "FALSE" &
    pancreas_sub$G2M == "FALSE" &
    pancreas_sub$Fancb_Expressed == "TRUE" &
    pancreas_sub$Dlg3_Expressed == "FALSE"
)