plotmulti: Generate all tepr plots for all experiment comparisons

Description

This function generates for all experiment comparisons contained in the object resteprmulti all plots of tepr: ECDF, auc, metagene, and histtoknee.

Usage

plotmulti(resteprmulti, expdf, ecdfgenevec, outfold = tempdir(), digits = 2,
middlewind = 100, pval = 0.01, colvec = c("#90AFBB", "#10AFBB",
"#FF9A04", "#FC4E07"), genaucvec = NA, aucaxisminx = -10,
aucaxismaxx = 100, aucaxisminy = -10, aucaxismaxy = 100, aucmaintitle = "",
aucsubtitle = "", auclegendpos = "bottom", formatname = "pdf",
uniname = "Universe", groupname = "Group", histkneexlim = NA,
binwidthvalhistknee = NA, verbose = TRUE)

Value

Nothing is returned. Figures are written to outfold in the subfolder of the corresponding comparison.

Arguments

resteprmulti: Result returned by the function teprmulti.
expdf: A data frame containing experiment data that should have columns named 'condition', 'replicate', 'strand', and 'path'.
ecdfgenevec: A vector specifying the names of the genes of interest to plot the ecdf of.
outfold: Path to the output folder where the plots will be written. Subfolders with the names of the comparisons are automatically created. Default is tempdir().
digits: For the ecdf plot, the number of decimal places to round the AUC and KS values. Default is 2.
middlewind: For the ecdf plot, the index of the middle window representing the region centered around the TSS. Default is 100.
pval: For the ecdf plot, a numeric value for the p-value threshold to determine the significance of the KS test. Default is 0.01.
colvec: For the ecdf plot, a vector of 4 colors used to distinguish the different conditions. Default is c("#90AFBB", "#10AFBB", "#FF9A04", "#FC4E07").
genaucvec: For the auc plot, vector of gene names to highlight, Used for the plot of type "pval". Default is NA. If left to NA, the plot taking into account the p-values is not generated.
aucaxisminx: For the auc plot, minimum value for the x-axis. Default is -10.
aucaxismaxx: For the auc plot, maximum value for the x-axis. Default is 100.
aucaxisminy: For the auc plot, minimum value for the y-axis. Default is -10.
aucaxismaxy: For the auc plot, maximum value for the y-axis. Default is 100.
aucmaintitle: For the auc plot, main title of the plot. Default is an empty string.
aucsubtitle: For the auc plot, subtitle of the plot. Default is an empty string.
auclegendpos: For the auc plot, position of the legend. Default is "bottom".
formatname: Format of the saved plot (e.g., "pdf", "png"). Default is "pdf".
uniname: Column name in the second element of resteprmulti representing the universe selection. Default is "Universe".
groupname: Column name in the second element of resteprmulti representing the type of group a transcript belong to. Default is "Group".
histkneexlim: For the plot histoknee, a numeric vector of length 2 specifying the limits of the x-axis. Default is NA, which automatically sets the limits based on plottype.
binwidthvalhistknee: For the plot histoknee, a numeric value for the width of the bins in the histogram. Default is NA, which automatically selects a bin width based on plottype.
verbose: A logical flag indicating whether to display detailed messages about the function's progress. Default is TRUE.

Details

The function goes through each element of resteprmulti which corresponds to a comparison of two conditions. For each element it calls the following functions: #'

"plotecdf": The function generates a figure for each gene given in ecdfgenevec.
"plotauc": Generates figures by groups and pval. The lattest figure is not generated if genaucvec = NA.
"plotmetagenes": Generates the figures by attenuation, outgroup, universe, and all.
"plothistoknee": Generate the figures by percent and kb.

Examples

Run this code

# Assuming resteprmulti is the object returned by the function teprmulti
# and expdf contains the necessary data:
if (FALSE) {
plotmulti(resteprmulti, expdf, ecdfgenevec = c("EGFR", "DAP", "FLI1"))}