plot_volcano: Create an interactive volcano plot

In j-andrews7/CRISPRball: Shiny Application for Interactive CRISPR Screen Visualization, Exploration, Comparison, and Filtering

Create an interactive volcano plot

Description

Create an interactive volcano plot for data with fold change and significance terms.

Usage

plot_volcano(
  res,
  xlim = 5,
  ylim = 5,
  fc.thresh = 0.5,
  fc.lines = TRUE,
  hover.info = NULL,
  sig.line = TRUE,
  h.id = "crispr",
  feat.term = "rows",
  sig.term = "fdr",
  lfc.term = "LFC",
  down.color = "#0026ff",
  up.color = "#ff0000",
  insig.color = "#A6A6A6",
  sig.thresh = 0.05,
  fs = NULL,
  sig.size = 6,
  insig.size = 5,
  sig.opacity = 1,
  insig.opacity = 0.5,
  label.size = 10,
  webgl = TRUE,
  webgl.ratio = 7,
  show.counts = TRUE,
  show.hl.counts = TRUE,
  counts.size = 8,
  highlight.featsets = NULL,
  highlight.feats = NULL,
  featsets = NULL,
  highlight.feats.color = "#E69F00",
  highlight.feats.size = 7,
  highlight.feats.opac = 1,
  highlight.feats.linecolor = "#000000",
  highlight.feats.linewidth = 1,
  highlight.feats.label = TRUE,
  highlight.featsets.color = "#009E73",
  highlight.featsets.size = 7,
  highlight.featsets.opac = 1,
  highlight.featsets.linecolor = "#000000",
  highlight.featsets.linewidth = 1,
  highlight.featsets.label = FALSE,
  h.id.suffix = "_volc"
)

Arguments

res	Dataframe containing, at minimum, fold change and significance values.
xlim	Positive numeric scalar indicating x-axis limits. The negative value will be used for the lower limit.
ylim	Positive numeric scalar indicating y-axis limits. The negative value will be used for the lower limit.
fc.thresh	Numeric scalar indicating the fold change threshold for coloring significant features.
fc.lines	Logical indicating whether to add fold change threshold lines to the plot.
hover.info	Character vector indicating which additional columns from res to include in the hover info.
sig.line	Logical indicating whether to add a significance threshold line to the plot.
h.id	Character scalar indicating the unique ID of the plotly object. Can usually be ignored, but should be used if multiple plots are being created in the same R session (e.g. Shiny app).
feat.term	Character scalar indicating the column name of the feature IDs in res.
sig.term	Character scalar indicating the column name of the significance values in res.
lfc.term	Character scalar indicating the column name of the log fold change values in res.
down.color	Character scalar indicating the color of down-regulated features.
up.color	Character scalar indicating the color of up-regulated features.
insig.color	Character scalar indicating the color of insignificant features.
sig.thresh	Numeric scalar indicating the significance threshold for coloring significant features.
fs	Dataframe containing coordinates and label information for points that should be labeled. Columns should be: x - x coordinate of the point y - y coordinate of the point customdata - label to be displayed
sig.size	Numeric scalar indicating the size of significant feature points.
insig.size	Numeric scalar indicating the size of insignificant feature points.
sig.opacity	Numeric scalar indicating the opacity of significant feature points.
insig.opacity	Numeric scalar indicating the opacity of insignificant feature points.
label.size	Numeric scalar indicating the size of feature labels.
webgl	Logical indicating whether to use WebGL for rendering the plot.
webgl.ratio	Numeric scalar indicating the ratio of WebGL to HTML5 canvas rendering, increases resolution of saved plot when WebGL plotting is not used.
show.counts	Logical indicating whether to show annotations for the number of features in the plot.
show.hl.counts	Logical indicating whether to show annotations for the number of highlighted features in the plot.
counts.size	Numeric scalar indicating the size of the feature counts labels.
highlight.featsets	Character vector indicating which feature sets should be highlighted.
highlight.feats	Character vector indicating which features should be highlighted.
featsets	Named list of feature sets to be used for highlighting.
highlight.feats.color	Character scalar indicating the color of highlighted features.
highlight.feats.size	Numeric scalar indicating the size of highlighted features.
highlight.feats.opac	Numeric scalar indicating the opacity of highlighted features.
highlight.feats.linecolor	Character scalar indicating the line color of highlighted features.
highlight.feats.linewidth	Numeric scalar indicating the line width of highlighted features.
highlight.feats.label	Logical indicating whether to label highlighted features.
highlight.featsets.color	Character scalar indicating the color of highlighted feature sets.
highlight.featsets.size	Numeric scalar indicating the point size of highlighted feature sets.
highlight.featsets.opac	Numeric scalar indicating the opacity of highlighted feature sets.
highlight.featsets.linecolor	Character scalar indicating the line color of highlighted feature sets.
highlight.featsets.linewidth	Numeric scalar indicating the line width of highlighted feature sets.
highlight.featsets.label	Logical indicating whether to label highlighted feature sets.
h.id.suffix	Character scalar indicating the suffix to be added to the plotly object ID.

Value

An interactive plotly volcano plot.

Author(s)

Jared Andrews

Examples

library(CRISPRball)
d1.genes <- read.delim(system.file("extdata", "esc1.gene_summary.txt",
    package = "CRISPRball"
), check.names = FALSE)
plot.df <- gene_ingress(d1.genes,
    sig.thresh = 0.05, es.thresh = 0.5,
    es.col = "LFC", sig.col = "fdr"
)
plot_volcano(plot.df, feat.term = "id")

j-andrews7/CRISPRball documentation built on Nov. 3, 2024, 5:11 a.m.