# Plot Histogram of Distance from TSS to Knee Point 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). ```r 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`. ## Returns 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. ## Examples ```r 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) ``` ## See Also [universegroup]

plothistoknee function