correlation.plots {ORFik}R Documentation

Correlation plots between all samples

Description

Get 3 correlation plots (1 simple (correlation colors), 2 complex with correlation value + dot plots of per gene ) of raw counts and log2(count + 1) over selected region in: c("mrna", "leaders", "cds", "trailers")

Usage

correlation.plots(
  df,
  output.dir,
  region = "mrna",
  type = "fpkm",
  height = 400,
  width = 400,
  size = 0.15,
  plot.ext = ".pdf",
  complex.correlation.plots = TRUE,
  data_for_pairs = countTable(df, region, type = type)
)

Arguments

df

an ORFik experiment

output.dir

directory to save to, 3 files named: cor_plot, cor_plot_log2 and cor_plot_simple with either .pdf or .png

region

a character (default: mrna), make raw count matrices of whole mrnas or one of (leaders, cds, trailers)

type

which value to use, "fpkm", alternative "counts".

height

numeric, default 400 (in mm)

width

numeric, default 400 (in mm)

size

numeric, size of dots, default 0.15.

plot.ext

character, default: ".pdf". Alternatives: ".png" or ".jpg". Note that in pdf format the complex correlation plots become very slow to load!

complex.correlation.plots

logical, default TRUE. Add in addition to simple correlation plot two computationally heavy dots + correlation plots. Useful for deeper analysis, but takes longer time to run, especially on low-quality gpu computers. Set to FALSE to skip these.

data_for_pairs

a data.table from ORFik::countTable of counts wanted. Default is fpkm of all mRNA counts over all libraries.

Value

invisible(NULL)


[Package ORFik version 1.14.7 Index]