plotmetagenes: Plot Metagenes for Gene Groups

In tepr: Transcription Elongation Profiling

Plot Metagenes for Gene Groups

Description

This function plots metagene profiles based on transcript data, comparing transcription density across conditions (e.g., control vs. stress). The function allows the user to plot metagenes for different gene groups such as attenuated genes, outgroup genes, the entire universe of genes, or all genes.

Usage

plotmetagenes(unigroupdf, dfmeandiff, expdf, plottype = "attenuation",
daucname = "dAUC_Diff_meanFx_HS_ctrl", auc_ctrlname = "AUC_ctrl",
auc_stressname = "AUC_HS", plot = FALSE, formatname = "pdf",
outfold = tempdir(), verbose = TRUE)

Arguments

unigroupdf	A data frame containing gene-level information, including group classifications and dAUC data for different conditions (see universegroup).
dfmeandiff	A data frame containing mean transcription values and coordinates for each transcript (see meandifference).
expdf	A data frame containing experiment data that should have columns named 'condition', 'replicate', 'strand', and 'path'.
plottype	A string specifying the group of genes to plot. Options are "attenuation", "outgroup", "universe", or "all". Default is "attenuation".
daucname	A string specifying the column name for the delta AUC value (difference between conditions). Default is "dAUC_Diff_meanFx_HS_ctrl".
auc_ctrlname	A string specifying the column name for the control condition AUC values. Default is "AUC_ctrl".
auc_stressname	A string specifying the column name for the stress condition AUC values. Default is "AUC_HS".
plot	A logical flag indicating whether to display the plot interactively (TRUE) or save it to a file (FALSE). Default is FALSE.
formatname	A string specifying the format of the saved plot file. Default is "pdf".
outfold	A string specifying the output folder where the plot will be saved if plot = FALSE. Default is the current directory.
verbose	A logical flag indicating whether to display detailed messages about the function's progress. Default is TRUE.

Details

This function summarizes mean transcription levels across genomic coordinates for different gene groups and plots the transcription density from the transcription start site (TSS) to the transcription termination site (TTS). The function can generate metagene plots for different gene groups such as attenuated, outgroup, or all genes, and compares transcription profiles between conditions (e.g., control vs. stress). The resulting plot helps visualize differences in transcriptional response between groups of genes under different conditions.

Value

A metagene plot comparing transcription density across conditions (e.g., control vs. stress) for the selected group of genes. The plot can either be displayed interactively or saved to a file.

See Also

[universegroup], [meandifference]

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 plotmetagenes
plotmetagenes(resug, resmeandiff, expdf, plottype = "attenuation", plot = TRUE)

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