plotauc: Plot AUC Comparison Between Conditions

Description

This function generates scatterplots comparing the area under the curve (AUC) for control and stress conditions, with an option to highlight specific genes or groups. The plot can be saved as a file or displayed interactively.

Usage

plotauc(tab, expdf, genevec = NA, auc_ctrlname = "AUC_ctrl",
auc_stressname = "AUC_HS",
pvalkstestcolname = "adjFDR_p_dAUC_Diff_meanFx_HS_ctrl",
labelx = "AUC in Control", labely = "AUC in Stress", axismin_x = -10,
axismax_x = 100, axismin_y = -10, axismax_y = 100, maintitle = "",
subtitle = "", legendpos = "bottom", formatname = "pdf", outfold = tempdir(),
outfile = "AUCcompare_pval", plottype = "pval", plot = FALSE,
universename = "Universe", groupname = "Group", verbose = TRUE)

Value

A plot comparing AUC values between control and stress conditions, either displayed or saved to a file.

Arguments

tab: A data frame containing the AUC values for control and stress conditions, and other columns required for plotting (e.g., p-values or group memberships, see allauc).
expdf: A data frame containing experiment data that should have columns named 'condition', 'replicate', 'strand', and 'path'.
genevec: A vector of gene names to highlight on the plot, applicable when plottype is set to "pval". Default is NA.
auc_ctrlname: The column name in tab for the AUC under control conditions. Default is "AUC_ctrl".
auc_stressname: The column name in tab for the AUC under stress conditions. Default is "AUC_HS".
pvalkstestcolname: The column name in tab for the adjusted FDR p-values from the KS test. Default is "adjFDR_p_dAUC_Diff_meanFx_HS_ctrl".
labelx: Label for the x-axis. Default is "AUC in Control".
labely: Label for the y-axis. Default is "AUC in Stress".
axismin_x: Minimum value for the x-axis. Default is -10.
axismax_x: Maximum value for the x-axis. Default is 100.
axismin_y: Minimum value for the y-axis. Default is -10.
axismax_y: Maximum value for the y-axis. Default is 100.
maintitle: Main title of the plot. Default is an empty string.
subtitle: Subtitle of the plot. Default is an empty string.
legendpos: Position of the legend. Default is "bottom".
formatname: Format of the saved plot (e.g., "pdf", "png"). Default is "pdf".
outfold: Output folder where the plot will be saved. Default is tempdir().
outfile: Name of the output file. Default is "AUCcompare_pval".
plottype: Type of plot to generate. Can be "pval" for p-value based plots or "groups" for group-based plots. Default is "pval".
plot: A logical flag indicating whether to display the plot interactively (TRUE) or save it to a file (FALSE). Default is FALSE.
universename: Column name in tab representing the universe group in group-based plots. Default is "Universe".
groupname: Column name in tab representing specific groups in group-based plots. Default is "Group".
verbose: A logical flag indicating whether to display detailed messages about the function's progress. Default is TRUE.

Details

The function supports two plot types:

"pval": The plot highlights genes based on adjusted FDR p-values and can highlight specific genes provided in genevec.
"groups": The plot highlights predefined groups, such as "Attenuated" and "Outgroup", within the data.

If plot = TRUE, the plot is displayed interactively. If plot = FALSE, the plot is saved to a file in the specified format and output folder.

Examples

Run this code

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, 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 plotauc
plotauc(resug, expdf, plottype = "groups", plot = TRUE)