Draw DDEGs from one biological pathway from two master.list objects and also show LOESS curve fitting for both experimental groups

Source: R/draw_CurveComp.R

For one specific biological pathway, compare its DDEGs from one experimental group to the other one. For example, if group 1 the most dynamic biological pathway from TimeHeatmap is GO term A, and there were 100 DDEGs identified from experimental group 1. We want to see how these DDEGs behave in the other experimental group. Maybe they are also dynamic, but activation/deactivation time may differ. This function will fit LOESS smooth curve fitting for each group and compare the trajectories visually.

draw_CurveComp(
  master.list.1,
  master.list.2,
  ht.1,
  pathway = "",
  group.1.name = "group1",
  group.2.name = "group2"
)

Arguments

master.list.1,

a list object. The output from run_TrendCatcher function, contains master.table element.

master.list.2,

a list object. The output from run_TrendCatcher function, contains master.table element.

ht.1,

TimeHeatmap object. The output from draw_TimeHeatmap_GO function, contains GO.df object.

pathway,

characters. Must be a biological pathway from GO.df, Description column.

group.1.name,

characters. For example, severe group. By default group1.

group.2.name,

characters. For example, moderate group. By default group2

Value

A ggplot object and plot.

Examples

if (FALSE) {
severe.path<-system.file("extdata", "MasterListSevere.rda", package = "TrendCatcher")
load(severe.path)
moderate.path<-system.file("extdata", "MasterListModerate.rda", package = "TrendCatcher")
load(moderate.path)
ht.path<-system.file("extdata", "htSevere.rda", package = "TrendCatcher")
load(ht.path)
g<-draw_CurveComp(master.list.1 = master.list.severe, master.list.2 = master.list.moderate, ht.1 = ht.severe, pathway = "neutrophil activation",group.1.name = "severe", group.2.name = "moderate")
print(g)
}