CP_PlotHeatmap: Title Heatmaps for Rhythmicity Signals

In XiangningXue/CircadianPipeline: What the Package Does (One Line, Title Case)

Title Heatmaps for Rhythmicity Signals

Description

Title Heatmaps for Rhythmicity Signals

Usage

CP_PlotHeatmap(
  x,
  genes.plot = NULL,
  col_breaks = c(seq(-2, 0, length = 100), seq(0.1, 1, length = 200), seq(1.1, 2,
    length = 200)),
  col_low_mid_high = c("blue", "yellow", "gold"),
  Info1 = "group I",
  Info2 = "group II",
  ...,
  filename = NULL,
  file.width = 8,
  file.height = 4
)

Arguments

x	CP_Rhythmicity() output
genes.plot	a vector of character strings. Names of genes to be plotted. Names should be same in nomenclature as gname in the data list. If NULL, the top 100 most rhythmic genes from group I will be used
col_breaks	color breaks
col_low_mid_high	color choice for the heatmaps
Info1	character string. Used in the plot title for group I.
Info2	character string. Used in the plot title for group II (if exist).
...	other argument to pass to ComplexHeatmap::Heatmap()
filename	character string of the filename for exporting. If NULL, plots are not saved.
file.width	height of the export plot
file.height	width of the export plot

Examples

x = CP_sim_data(ngene=1000, nsample=30, A1=c(1, 3), A2=c(1, 3),
phase1=c(0, pi/4), phase2=c(pi/4, pi/2),
M1=c(4, 6), M2=c(4, 6), sigma1=1, sigma2=1)

rhythm.res = CP_Rhythmicity(x1 = x[[1]], x2 = x[[2]])
CP_PlotHeatmap(rhythm.res)

XiangningXue/CircadianPipeline documentation built on May 3, 2022, 3:04 p.m.