Testing for RNA dropout of a 4sU sample is performed by comparing half-lives or NTR ranks against the log2 fold change of the 4sU sample vs equivalent no4sU samples.
Usage
Plot4sUDropoutRankAll(data, pairs = Findno4sUPairs(data), ...)
Plot4sUDropoutAll(data, pairs = Findno4sUPairs(data), ...)
Plot4sUDropoutDeferAll(data, pairs = NULL, ...)
Plot4sUDropoutRankDeferAll(data, pairs = NULL, ...)
Plot4sUDropoutRank(
data,
w4sU,
no4sU = Findno4sUPairs(data)[[w4sU]],
ntr = w4sU,
ylim = NULL,
LFC.fun = lfc::PsiLFC,
slot = "count",
correction = 1,
label.corr = TRUE,
return.corr = FALSE,
boxplot.bins = 10,
title = w4sU,
size = 1.5,
invert.ranks = FALSE
)
Plot4sUDropout(
data,
w4sU,
no4sU = Findno4sUPairs(data)[[w4sU]],
ntr = w4sU,
ylim = NULL,
LFC.fun = lfc::PsiLFC,
slot = "count",
hl.quantile = 0.8,
hl = NULL,
correction = 1,
label.corr = FALSE,
return.corr = FALSE,
title = w4sU,
size = 1.5,
color.by.ntr = FALSE
)Arguments
- data
a grandR object
- pairs
a no4sU pairs list as generated by Findno4sUPairs
- ...
further arguments to be passed to or from other methods.
- w4sU
the name of a 4sU sample
- no4sU
the name(s) of equivalent no4sU sample(s)
- ntr
the name of a sample to take NTRs from (usually equal to w4sU)
- ylim
y axis limits
- LFC.fun
function to compute log fold change (default: PsiLFC, other viable option: NormLFC)
- slot
the slot of the grandR object to take the data from; for PsiLFC, this really should be "count"!
- correction
correction factor
- label.corr
add statistics as subtitle
- return.corr
instead of only the ggplot object, return a list with slots plot (what is normally returned) and label (the correlation statistics)
- boxplot.bins
how many boxplots for
Plot4sUDropoutRank- title
the main title for the plot
- size
the point size
- invert.ranks
if TRUE, left to right on the plot is largest NTR to smallest NTR
- hl.quantile
the half-life quantile to cut the plot
- hl
if NULL, compute half-lives from the ntr column; otherwise, must be a vector containing half-lives
- color.by.ntr
if true, compute the density colors along the ntr axis instead of globally
Value
either a ggplot object, a list of ggplot objects, or a list of deferred functions for plotting
Details
The deferred versions are useful to be used in conjunction with ServeGrandR plot.static. Their implementation make sure that they are lightweight, i.e. when saving the returned function to an Rdata file, the grandR object is not stored.