correlation.plots {ORFik} | R Documentation |
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")
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) )
df |
an ORFik |
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. |
invisible(NULL)