plotRatioDensity: plotRatioDensity Function to plot density of ratios between...

In avastermark19/doseR_0.99.4: doseR

Description

This function plots the expression of the supplied countDat object, using ratios between a pair of selected treatments.

Usage

plotRatioDensity(cD, groupings= NULL, treatment1=NULL,
treatment2=NULL, mode_mean=TRUE, LOG2=TRUE,...)

Arguments

cD	A countDat object.
groupings	A grouping (annotation column), e.g. groupings="something".
treatment1	Symbol, treatment 1.
treatment2	Symbol, treatment 2.
mode_mean	Boolean, Calculate RowMeans or RowMedians.
LOG2	Boolean, Calculate LOG2.
...	Passthrough arguments to boxplot (additional arguments affecting the summary produced).

Details

This function plots expression of the supplied countDat object using ratios of treatment1/treatment2.

Value

Returns an invisible data frame containing the x-values and corresponding density for each applicable annotation column entry.

Author(s)

AJ Vaestermark, JR Walters.

References

The "doseR" package, 2018 (in press).

Examples

data(hmel.data.doser)
reps <- c("Male", "Male", "Male", "Female", "Female", "Female")
annotxn <- data.frame("Chromosome" = factor(hmel.dat$chromosome,
levels = 1:21))
annotxn$ZA <- factor(ifelse(hmel.dat$chromosome == 21, "Z", "A"),
levels = c("A", "Z"))
hm.tr<-hmel.dat$trxLength
hm<-new("countDat",data=hmel.dat$readcounts,seglens=hm.tr,
annotation=annotxn)
replicates(hm) <- reps
libsizes(hm) <- getLibsizes2(hm, estimationType = "total")
rpkm(hm) <- make_RPKM(hm)
plotRatioDensity(hm, groupings='ZA', treatment1 = 'Male',
treatment2 = 'Female',lty=1,type="l")

avastermark19/doseR_0.99.4 documentation built on May 6, 2019, 12:08 p.m.