plothistoknee: Plot Histogram of Distance from TSS to Knee Point

In tepr: Transcription Elongation Profiling

Plot Histogram of Distance from TSS to Knee Point

Description

This function generates a histogram showing the distribution of the distance from the transcription start site (TSS) to the knee point for attenuated genes. The distance can be plotted either as a percentage of the gene length or in kilobases (kb).

Usage

plothistoknee(unigroupdf, plottype = "percent", xlimvec = NA,
binwidthval = NA, kneename = "knee_AUC_HS", plot = FALSE, outfold = tempdir(),
formatname = "pdf", universename = "Universe", groupname = "Group",
verbose = TRUE)

Arguments

unigroupdf	A data frame containing gene-level statistics, including knee point data and group classification (see universegroup).
plottype	A string specifying the type of distance to plot. Options are "percent" for the percentage of the gene or "kb" for distance in kilobases. Default is "percent".
xlimvec	A numeric vector of length 2 specifying the limits of the x-axis. Default is NA, which automatically sets the limits based on plottype.
binwidthval	A numeric value for the width of the bins in the histogram. Default is NA, which automatically selects a bin width based on plottype.
kneename	A string specifying the name of the column in unigroupdf that contains the knee point data. Default is "knee_AUC_HS".
plot	A logical flag indicating whether to display the plot interactively (TRUE) or save it to a file (FALSE). Default is FALSE.
outfold	A string specifying the output folder where the plot will be saved if plot = FALSE. Default is the current directory.
formatname	A string specifying the format of the saved plot file. Default is "pdf".
universename	A string specifying the name of the column in unigroupdf that defines the universe of genes. Default is "Universe".
groupname	A string specifying the name of the column in unigroupdf that defines the group classification of genes. Default is "Group".
verbose	A logical flag indicating whether to display detailed messages about the function's progress. Default is TRUE.

Value

A histogram showing the distribution of the distance from the TSS to the knee point for attenuated genes. The plot can either be displayed interactively or saved to a file.

See Also

[universegroup]

Examples

exppath <-  system.file("extdata", "exptab.csv", package="tepr")
transpath <- system.file("extdata", "cugusi_6.tsv", package="tepr")
expthres <- 0.1

## Calculating necessary results
expdf <- read.csv(exppath)
transdf <- read.delim(transpath, header = FALSE)
avfilt <- averageandfilterexprs(expdf, transdf, expthres,
        showtime = FALSE, verbose = FALSE)
rescountna <- countna(avfilt, expdf, nbcpu = 1, verbose = FALSE)
ecdf <- genesECDF(avfilt, expdf, verbose = FALSE)
resecdf <- ecdf[[1]]
nbwindows <- ecdf[[2]]
resmeandiff <- meandifference(resecdf, expdf, nbwindows,
    verbose = FALSE)
bytranslistmean <- split(resmeandiff, factor(resmeandiff$transcript))
resknee <- kneeid(bytranslistmean, expdf, verbose = FALSE)
resauc <- allauc(bytranslistmean, expdf, nbwindows, verbose = FALSE)
resatt <- attenuation(resauc, resknee, rescountna, bytranslistmean, expdf,
        resmeandiff, verbose = FALSE)
resug <- universegroup(resatt, expdf, verbose = FALSE)

## Testing plothistoknee
plothistoknee(resug, plot = TRUE)

tepr documentation built on June 8, 2025, 10:46 a.m.