cnaParamsPlot: Plot CNA parameters to evaluate cell CNAs

In jlaffy/infercna: Infer Copy Number Alterations And Clonality In (Single-Cell) RNA-seq Data

Plot CNA parameters to evaluate cell CNAs

Description

Plot cells according to their CNA correlation and CNA signal values, and display this as a contour plot. If a "sample" column is provided, the resulting plot will be faceted by sample, with the sample name written in the plot. A "group" column is currently required (suggested to just make a group column with all values the same if there are no real groups annotated).

Usage

cnaParamsPlot(
  data,
  x,
  y,
  group = NULL,
  points = TRUE,
  point.col = "black",
  point.alpha = 0.075,
  point.size = 0.5,
  xlab = "CNA correlation",
  ylab = "CNA signal",
  xlim = NULL,
  ylim = NULL,
  xintercept = NULL,
  yintercept = NULL,
  bins = 30,
  breaks = scales::breaks_pretty(n = 4),
  xbreaks = breaks,
  ybreaks = ggplot2::waiver(),
  contour = TRUE,
  geom = "polygon",
  legend.justification = "right",
  legend.position = "top",
  legend.title = ggplot2::waiver(),
  cols = c("red", "blue"),
  text.size = 16,
  label.hjust = 1.25,
  label.vjust = 1.25,
  label.size = 5,
  ...
)

Arguments

data	data.frame with x (CNA correlations), y (CNA signals), group (e.g. presumed Malignant versus Reference Normal) and (optional) sample columns
x	column name corresponding to x values. Either passed as a string or as an unquoted column name. eg 'x' or x is fine.
y	column name corresponding to y values. Either passed as a string or as an unquoted column name. eg 'y' or y is fine.
group	column name corresponding to groups. Either passed as a string or as an unquoted column name. eg 'group' or group is fine.
points	logical; should cell points be plotted as well as the contour plot? Default: TRUE
point.col	relevant only if points = TRUE. specify point colour. Default: 'black'
point.alpha	relevant only if points = TRUE. specify point transparency. Default: 0.075
point.size	relevant only if points = TRUE. specify point size. Default: 0.5
xlab	x-axis title. Default: 'CNA correlation'
ylab	y-axis title. Default: 'CNA signal'
xlim	x-axis limits. Default: NULL
ylim	y-axis limits. Default: NULL
xintercept	PARAM_DESCRIPTION, Default: NULL
yintercept	PARAM_DESCRIPTION, Default: NULL
bins	number of bins to use for contour levels. Fewer bins averages over more of the data but often results with a 'cleaner' looking contour. Default: 7
breaks	breaks. Default: scales::breaks_pretty(n = 4)
xbreaks	x-axis breaks. Default: breaks
ybreaks	y-axis breaks. Default: ggplot2::waiver()
contour	contour lines as well as filled in contour areas? Default: TRUE
geom	I've only used polygon in this specific function but you can go crazy and try other things. Default: 'polygon'
legend.justification	legend justification. Default: 'right'
legend.position	legend position. set to 'none' if not desired. Default: 'top'
legend.title	legend title Default: ggplot2::waiver()
cols	colours of each group. Note that if more than two groups are present, more colours should be provided than the default two. Default: c("red", "blue")
text.size	base text size. Default: 16
label.hjust	only relevant if sample column in data. Adjust position of geom_text with sample name. Default: 1.25
label.size	only relevant if sample column in data. geom_text label size. Default: 5
...	other arguments passed to ggplot2::facet_wrap(.~sample, ...) if sample column in data.

Value

ggplot2 object

See Also

breaks_pretty waiver,tidyeval,ggplot,aes,geom_point,geom_density_2d,geom_label,scale_continuous,scale_alpha,scale_manual,theme,margin,c("guide_bins", "guide_colourbar", "guide_coloursteps", "guide_legend", "guides", "guides"),guide_legend,facet_wrap

jlaffy/infercna documentation built on Jan. 26, 2024, 11:24 p.m.