plot_error_volcano: Creates a scatterplot with optional errorbars and fine...

In Benjamin-Vincent-Lab/binfotron: Binfotron Bioinformatics Analysis Tools Suite

Creates a scatterplot with optional errorbars and fine control over labels, colors, alpha and more

Description

Creates a scatterplot with optional errorbars and fine control over labels, colors, alpha and more

Usage

plot_error_volcano(
  plot_df,
  axis_clm_x,
  axis_clm_y,
  alpha_clm = NA,
  color_clm = NA,
  color_scheme = scale_color_viridis_d(option = "rocket", begin = 0.8, end = 0.1),
  error_clm_lower = NA,
  error_clm_upper = NA,
  gg_add_on = theme_minimal(),
  independent_clm = NA,
  lab_color = "Q-Value",
  lab_x = "Hazard Ratio (Log10)",
  lab_y = "Uncorrected Significance (-Log10)",
  label_clm = NA,
  label_nudge_x = 0.025,
  label_nudge_y = -0.15,
  label_size = 1.5,
  max_labels = 20,
  output_path = NA,
  plot_title = "Significance vs. Hazard Ratio",
  size_height = 4.5,
  size_width = 6
)

Arguments

plot_df	Dataframe containing at a minimum x and y axis data
axis_clm_x	column name in plot_df corresponding to x axis
axis_clm_y	column name in plot_df corresponding to y axis
alpha_clm	column name of categorical or continuous variable in plot_df on which to base alpha aesthetic
color_clm	column name of categorical variable in plot_df on which to base color aesthetic
color_scheme	ggplot function to specify discrete colors
error_clm_lower	column name containing lower bound of error bars
error_clm_upper	column name containing upper bound of error bars
gg_add_on	ggplot elements to add on to plot. Defaults to theme_minimal()
independent_clm	column name in plot_df from which to pull values for reporting on removed extreme values. If not set, and extreme values are removed, only the number of removed observations will be reported.
lab_color	String for labeling color legend
lab_x	String for labeling x axis
lab_y	String for labeling y axis
label_clm	column name in plot_df from which to pull labels for points
label_size	numeric value to use for the size of the point labels
max_labels	Integer to set the max number of labels that will be shown
output_path	Output path for plot
plot_title	String for plot title
size_height	Numeric to specify plot height
size_width	Numeric to specify plot width

Value

Returns ggplot object with point and optionally errorbar geoms as well as point labels if desired

Benjamin-Vincent-Lab/binfotron documentation built on Oct. 1, 2024, 8:33 p.m.