plot_ma: Highchart version of MA-plot

In HuntsmanCancerInstitute/hciR: RNA-seq workflows at HCI

Highchart version of MA-plot

Description

Plot mean normalized counts and fold changes in an interactive MA-plot

Usage

plot_ma(
  res,
  signif = 0.05,
  baseMean = 10000,
  foldchange = 2,
  radius = 3,
  size = 1,
  alpha = 0.3,
  sig_alpha = TRUE,
  ylab = "Log2 Fold Change",
  ggplot = TRUE,
  ...
)

Arguments

res	Annotated DESeq results table from results_all
signif	significance level, default 0.05
baseMean	normalized count cutoff for labeling points, default 10000
foldchange	absolute value of log2 fold change cutoff for labeling points, default 2
radius	highchart point size, default 3
size	ggplot point size, default 1
alpha	ggplot alpha transparency, default 0.3
sig_alpha	use transparency for significant genes, default TRUE
ylab	y-axis label
ggplot	plot ggplot version
...	other options like width passed to hc_chart

Value

A highchart or ggplot. Only points above the baseMean or log2 fold change cutoffs have mouseover labels.

Author(s)

Chris Stubben

Examples

plot_ma(pasilla$results, ggplot=TRUE)

HuntsmanCancerInstitute/hciR documentation built on Dec. 10, 2024, 12:22 p.m.