plot_effects: Plot cancer effects
In Townsend-Lab-Yale/cancereffectsizeR: Calculate Cancer Effect Size

plot_effects

R Documentation

Plot cancer effects

Description

Visualize and compare cancer effects for variants of interest.

Usage

plot_effects(
  effects,
  topn = 30,
  group_by = "variant",
  title = "",
  x_title = NULL,
  y_title = NULL,
  y_label = "auto",
  color_by = "darkseagreen4",
  color_label = NULL,
  legend.position = "right",
  legend_size_name = "auto",
  legend_color_name = NULL,
  viridis_option = "cividis",
  legend_size_breaks = "auto",
  label_individual_variants = TRUE,
  order_by_effect = TRUE,
  prevalence_method = "auto",
  show_ci = TRUE
)

Arguments

`effects`	Cancer effects table, as produced by `ces_variant()`. You can combine multiple tables via rbind() to plot multiple effects per variant, such as to compare effects across subgroups.
`topn`	Include up to this many variants. The highest-effect variants are plotted. (Or, if `group_by` is gene, include up to this many groups. Groups are ranked by their highest-effect variants.)
`group_by`	If 'variant' (the default), one variant per row in the plot. If "gene" or some other column name, variants will be plotted together accordingly.
`title`	Main title for the plot (by default, no title)
`x_title`	Text for the X-axis label.
`y_title`	Text for the Y-axis label.
`y_label`	Y-axis labels for each group of variants. By default ("auto"), will be variant names when `group_by = "variant"`, and the values in the group_by column otherwise.
`color_by`	A single color to use for geom_point fill (default "darkseagreen4"). Or, the name of a column that specifies color groupings. Can be used to distinguish points when multiple effects are plotted per variant (for example, when comparing effects between subgroups), or to highlight related groups of variants. A viridis color scale will be applied, unless ever single value in the color column is interpretable as an R color, in which case the given colors will be used.
`color_label`	If color_by is supplying color names for scale_color_identity(), optionally include color_label so that colors can be labeled in the plot legend.
`legend.position`	Passed to ggplot's legend.position (none, left, right, top, bottom, or coordinates). Use "none" to eliminate the legend. Defaults to "right".
`legend_size_name`	The title for the point size scale (larger points = more prevalent variants).
`legend_color_name`	The title for the point fill color scale.
`viridis_option`	If using `color_by`, this argument specifies which viridis color map to use. Ignored if you specify your own colors.
`legend_size_breaks`	Vector of specific mutation counts (or percentages) to depict in the point size legend. Specify numeric values if you don't like what gets produced by the default ("auto"). Set to FALSE or to a single desired point size to turn of size scaling.
`label_individual_variants`	When TRUE (default), individual variants within groups will be labeled when group_by is not 'variant'. Set FALSE to not label variants, or specify a column name that supplies a label for each row in the effects table. By default, variant names will be used for labels. If group_by is exactly "gene", labels will be shortened to just the amino acid changes. Some labels will be omitted (with a warning) if it seems there are too many to display in the plot space.
`order_by_effect`	When TRUE (default), variants are plotted in order of effect. When FALSE, variants are plotted top-down in the order they are supplied.
`prevalence_method`	Show each variant's prevalence as a raw mutation count ("count", the default), or as a percentage of samples with sequencing coverage at the site ("percent"). If the effects table has the same number of samples covering every inference, you can choose "both".
`show_ci`	TRUE/FALSE to depict confidence intervals in plot (default TRUE).