draw_GOHeatmap: Draw GOHeatmap containing Terms from TimeHeatmap and included...

In jaleesr/TrendCatcher_1.0.0: TrendCatcher: A Versitile R package for analyse longitudinal RNA-seq study

Draw GOHeatmap containing Terms from TimeHeatmap and included Genes

Description

This funcitons takes the master.list output from run_TrendCatcher, and merge.df output from draw_TimeHeatmap_GO and draw_TimeHeatmap_enrichR. And showing all the genes used for enrichment analysis and their logFC compared to previous break point.

Usage

draw_GOHeatmap(
  master.list,
  time.window = "",
  go.terms = "",
  merge.df = NA,
  logFC.thres = 2,
  figure.title = "",
  save.tiff.path = NA,
  tiff.res = 100,
  tiff.width = 1500,
  tiff.height = 1500
)

Arguments

master.list,	a list object. The output from run_TrendCatcher function, contains master.table element.
time.window,	a character. Must be one of the merge.df$t.name.
go.terms,	a character array. Must be an array of go terms from the merge.df$Description.
merge.df,	a dataframe. The output dataframe from output list of draw_TimeHeatmap_GO or draw_TimeHeatmap_enrichR. Use $merge.df to obtain it.
logFC.thres,	a numeric variable. The logFC threshold compared to each genes previous break point expression level. By default is 2, meaning for each gene, the current time window's expression level is 2-fold compared to previous break point's expression level.
figure.title,	character
save.tiff.path,	by default is NA
tiff.res,	resolution
tiff.width,	figure width
tiff.height,	figure height

Value

A list object, including elements named GOheatmap and GOheatmapDat. GOheatmap is a ComplexHeatmap object for figure. GOheatmapDat is a data.frame include log2FC value of each gene's expression change compared to the previous break point.

Examples

## Not run: 
example.file.path<-system.file("extdata", "BrainMasterList.rda", package = "TrendCatcher")
load(example.file.path)
time_heatmap<-draw_TimeHeatmap_GO(master.list = master.list)
merge.df<-time_heatmap$merg.df
time.window<-"0h-6h"
go.terms<-c("regulation of defense response", "leukocyte migration", "myeloid leukocyte migration", "leukocyte chemotaxis",
"granulocyte chemotaxis", "cellular response to chemokine", "chemokine-mediated signaling pathway", "angiogenesis", "sprouting angiogenesis",  "respone to bacterium", "leukocyte mediated immunity")
go.df<-draw_GOHeatmap(master.list = master.list, time.window = "0h-6h", go.terms = go.terms, merge.df = merge.df, logFC.thres = 2)

## End(Not run)

jaleesr/TrendCatcher_1.0.0 documentation built on Jan. 29, 2024, 9:34 p.m.