ivolcano (version 0.0.4)

ivolcano_point: ivolcano_point

Description

Visualize points in volcano plot

Usage

ivolcano_point(
  data,
  logFC_col = "logFC",
  pval_col = "adj.P.Val",
  gene_col = "gene",
  title = "Volcano Plot",
  interactive = TRUE,
  onclick_fun = NULL,
  pval_cutoff = 0.05,
  logFC_cutoff = 1,
  pval_cutoff2 = NULL,
  logFC_cutoff2 = NULL,
  size_by = "none",
  point_size = list(base = 2, medium = 4, large = 6)
)

Value

base plot of a volcano plot

Arguments

data

A data frame that contains minimal information with gene id, logFC and adjusted P values

logFC_col

column name in 'data' that stored the logFC values

pval_col

column name in 'data' that stored the adjusted P values

gene_col

column name in 'data' that stored the gene IDs

title

plot title

interactive

whether plot the graph in interactive mode

onclick_fun

effects when click on the dot (gene), default is NULL

pval_cutoff

cutoff of the adjusted P values

logFC_cutoff

cutoff of the logFC values

pval_cutoff2

second cutoff of the adjusted P values for advanced mode

logFC_cutoff2

second cutoff of the logFC values for advanced mode

size_by

one of "none" (default), "manual" (set by point_size), "negLogP", "absLogFC", or other variable in the input data to scale dot sizes.

point_size

set point size when size_by is "manual", a list with three elements: base, medium, large.