te_rna.plot {ORFik} | R Documentation |
Create TE plot of:
- Within sample (TE log2 vs mRNA fpkm)
te_rna.plot( dt, output.dir = NULL, filter.rfp = 1, filter.rna = 1, plot.title = "", plot.ext = ".pdf", width = 6, height = "auto", dot.size = 0.4, xlim = c(filter.rna, filter.rna + 2.5) )
dt |
a data.table with the results from |
output.dir |
a character path, default NULL(no save), or a directory to save to a file will be called "TE_within.pdf" |
filter.rfp |
numeric, default 1. What is the minimum fpkm value? |
filter.rna |
numeric, default 1. What is the minimum fpkm value? |
plot.title |
title for plots, usually name of experiment etc |
plot.ext |
character, default: ".pdf". Alternatives: ".png" or ".jpg". |
width |
numeric, default 6 (in inches) |
height |
a numeric, width of plot in inches. Default "auto". |
dot.size |
numeric, default 0.4, size of point dots in plot. |
xlim |
numeric vector of length 2. X-axis limits. Default:
|
a ggplot object
Other DifferentialExpression:
DEG.plot.static()
,
DTEG.analysis()
,
DTEG.plot()
,
te.table()
df <- ORFik.template.experiment() df.rfp <- df[df$libtype == "RFP",] df.rna <- df[df$libtype == "RNA",] #dt <- te.table(df.rfp, df.rna) #te_rna.plot(dt, filter.rfp = 0, filter.rna = 5, dot.size = 1)