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Plot tAge transcriptomic aging-clock predictions

Source: R/tAgePlot.R
tAgePlot.Rd

Plot tAge transcriptomic aging-clock predictions

Usage

tAgePlot(
  object,
  score_col = NULL,
  group.by = NULL,
  split.by = NULL,
  tool_name = "tAge",
  plot_type = c("box"),
  palette = "Chinese",
  palcolor = NULL,
  alpha = 1,
  point_size = 2.2,
  point_alpha = 0.85,
  box_alpha = 0.15,
  flip = TRUE,
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  theme_use = "theme_scop",
  theme_args = list(),
  legend.position = "none",
  legend.direction = "vertical",
  grid_major = TRUE,
  grid_major_colour = "grey80",
  grid_major_linetype = 2,
  grid_major_linewidth = 0.3,
  aspect.ratio = NULL,
  seed = 11,
  verbose = TRUE,
  ...
)

Arguments

object

A Seurat object returned by RuntAge() or a data frame with tAge prediction columns.

score_col

Prediction column to plot. If NULL, the first column ending in "_tAge" is used.

group.by

Column used to group predictions on the y axis.

split.by

An optional column to split the plot into facets.

tool_name

Name of the Seurat tool entry containing tAge results.

plot_type

Plot type. Currently "box" draws a boxplot with jittered pseudobulk samples.

palette, palcolor

Palette forwarded to thisplot::palette_colors().

alpha

Overall point and box alpha. point_alpha and box_alpha take precedence when set.

point_size, point_alpha

Jittered point size and alpha.

box_alpha

Boxplot fill alpha.

flip

Whether to flip coordinates so group labels run along the y axis. Default is TRUE.

title, subtitle, xlab, ylab

Plot labels.

theme_use

Theme function name. Default is "theme_scop", which maps to thisplot::theme_this(), matching the style used by thisplot::StatPlot().

theme_args

Additional arguments passed to theme_use.

legend.position, legend.direction

Legend position and direction. Default is "none".

grid_major

Whether to show major panel grid lines.

grid_major_colour, grid_major_linetype, grid_major_linewidth

Appearance of major panel grid lines.

aspect.ratio

Aspect ratio of the plot (y / x).

seed

RNG seed for jitter reproducibility.

verbose

Whether to print the message. Default is TRUE.

...

Reserved for future use.

Value

A ggplot object.

See also

RuntAge

Examples

if (FALSE) { # \dontrun{
pancreas_sub <- RuntAge(pancreas_sub, group.by = "CellType")
tAgePlot(pancreas_sub, group.by = "CellType")
} # }