pcaExperiment {ORFik} | R Documentation |
Detect outlier libraries with PCA analysis. Will output PCA plot of PCA component 1 (x-axis) vs PCA component 2 (y-axis) for each library (colored by library), shape by replicate. Will be extended to allow batch correction in the future.
pcaExperiment( df, output.dir = NULL, table = countTable(df, "cds", type = "fpkm"), title = "CDS fpkm (All genes)", plot.ext = ".pdf" )
df |
an ORFik |
output.dir |
default NULL, else character path to directory. File saved as "PCAplot_(experiment name)(plot.ext)" |
table |
data.table, default countTable(df, "cds", type = "fpkm"), a data.table of counts per column (default normalized fpkm values). |
title |
character, default "CDS fpkm (All genes)". |
plot.ext |
character, default: ".pdf". Alternatives: ".png" or ".jpg". Note that in pdf format the complex correlation plots become very slow to load! |
ggplot or invisible(NULL) if output.dir is defined or < 3 samples