tmodPanelPlot: Plot a summary of multiple tmod analyses

Description

Plot a summary of multiple tmod analyses

Usage

tmodPanelPlot(x, pie = NULL, clust = "qval", filter.empty.cols = FALSE,
  filter.empty.rows = TRUE, filter.unknown = TRUE, filter.by.id = NULL,
  col.labels = NULL, row.labels = NULL, pval.thr = 10^-2,
  plot.func = NULL, grid = "at", pie.colors = c("#0000FF", "#cccccc",
  "#FF0000"), plot.cex = 1, text.cex = 1, pie.style = "pie",
  col.labels.style = "top", legend.style = "auto", ...)

Arguments

list, in which each element has been generated with a tmod test function

pie

a data frame or a three-dimensional array with information for drawing a pie chart

clust

whether, in the resulting data frame, the modules should be ordered by clustering them with either q-values ("qval") or the effect size ("effect"). If NULL, the modules are sorted alphabetically by their ID.

filter.empty.cols

If TRUE, all elements (columns) with no significant enrichment in any row will be removed

filter.empty.rows

If TRUE, all modules (rows) with no significant enrichment in any column will be removed

filter.unknown

If TRUE, modules with no annotation will be omitted

filter.by.id

if provided, show only modules with IDs in this character vector

col.labels

Labels for the columns. If NULL, names of the elements of the list x will be used.

row.labels

Labels for the modules. This must be a named vector, with module IDs as vector names. If NULL, module titles from the analyses results will be used.

pval.thr

Results with p-value above pval.thr will not be shown

plot.func

Optionally, a function to be used to draw the dots. See "pvalEffectPlot"

grid

Style of a light-grey grid to be plotted; can be "none", "at" and "between"

pie.colors

character vector of length equal to the cardinality of the third dimension of the pie argument.

plot.cex

a numerical value giving the amount by which the plot symbols will be maginfied

text.cex

a numerical value giving the amount by which the plot text will be magnified, or a vector containing three cex values for row labels, column labels and legend, respectively

pie.style

Can be either "pie" or "rug"

col.labels.style

Style of column names: "top" (default), "bottom", "both", "none"

legend.style

Style of the legend: "auto" -- automatic; "broad": pval legend side by side with effect size legend; "tall": effect size legend above pval legend

...

Any further arguments will be passed to the pvalEffectPlot function

Value

a data frame with a line for each module encountered anywhere in the list x, two columns describing the module (ID and module title), and two columns(effect size and q value) for each element of list x.

Details

This function is useful if you run an analysis for several conditions or time points and would like to summarize the information on a plot. You can use lapply() to generate a list with tmod results and use tmodPanelPlot to visualize it.

tmodPanelPlot shows a heatmap-like plot. Each row corresponds to one module, and columns correspond to the time points or conditions for which the tmod analyses were run. Each significantly enriched module is shown as a red dot. Size of the dot corresponds to the effect size (for example, AUC in the CERNO test), and intensity of the color corresponds to the q-value.

By default, tmodPanelPlot visualizes each the results of a single statistical test by a red dot. However, it is often interesting to know how many of the genes in a module are significantly up- or down regulated. tmodPanelPlot can draw a pie chart based on the optional argument "pie". The argument must be a list of length equal to the length of x. Objects returned by the function tmodDecideTests can be directly used here. The rownames of either the data frame or the array must be the module IDs.

Examples

Run this code

data(Egambia)
E <- Egambia[,-c(1:3)]
pca <- prcomp(t(E), scale.=TRUE)

# Calculate enrichment for first 5 PCs
gs   <- Egambia$GENE_SYMBOL
gn.f <- function(r) {
    o <- order(abs(r), decreasing=TRUE)
    tmodCERNOtest(gs[o],
                qval=0.01)
}
x <- apply(pca$rotation[,3:4], 2, gn.f)
tmodPanelPlot(x, text.cex=0.7)