Subset TimeHeatmap by providing a manually selected non-redundant GO terms

Some GO terms are redundant. Users can manually select GO terms that are shown in the GO.df element in the TimeHeatmap object and show the TimeHeatmap figure.

draw_TimeHeatmap_selGO(
  time_heatmap,
  sel.go,
  master.list,
  GO.perc.thres = 0,
  nDDEG.thres = 0,
  term.width = 80,
  figure.title = "",
  save.tiff.path = NA,
  tiff.res = 100,
  tiff.width = 1500,
  tiff.height = 1500
)

Arguments

time_heatmap,

a list, the output of draw_TimeHeatmap_GO function. A TimeHeatmap object, with GO.df element included.

sel.go,

a character variable. An array of character names of GO terms, that match the GO terms from the Description column of GO.df.

master.list,

a list, the output of run_TrendCatcher function, a master.list object.

GO.perc.thres,

a numeric variable. A threshold to filter out GOs that only a little percentage of the genes are DDEGs. By default is 0.

nDDEG.thres,

an integer variable. A threshold to filter out GOs that only a small number of genes included. By default is 0.

term.width,

an integer variable. The character length for each GO term. If one GO term is super long, we can wrap it into term.width of strings into multiple rows. By default is 80.

figure.title,

a character variable. The main title of TimeHeatmap.

save.tiff.path,

a character variable, the file path to save the TIFF figure. If set to NA, it will plot it out. By default is NA.

tiff.res,

a numeric variable, the resolution of the TIFF figure. By default is 100.

tiff.width,

a numeric variable, the width of the TIFF figure. By default is 1500.

tiff.height,

a numeric variable, the height of the TIFF figure. By default is 1500.

Value

A list object, including elements names time.heatmap, merge.df and GO.df. time.heatmap is the ComplexHeatmap object. merge.df includes all the GO enrichment result and their activation/deactivation time window. GO.df includes GO enrichment used for plot TimeHeatmap and all the individual genes within each time window.

Examples

if (FALSE) {
example.file.path<-system.file("extdata", "BrainMasterList.rda", package = "TrendCatcher")
load(example.file.path)
gene.symbol.df<-get_GeneEnsembl2Symbol(ensemble.arr = master.list$master.table$Gene)
time_heatmap<-draw_TimeHeatmap_GO(master.list = master.list)
go.terms<-unique(time_heatmap$GO.df$Description)[1:5]
time_heatmap_selGO<-draw_TimeHeatmap_selGO(time_heatmap = time_heatmap, sel.go = go.terms, master.list = master.list, GO.perc.thres = 0, nDDEG.thres = 0, save.tiff.path = NA)
}