CP_PlotPeakHist: Plot histogram for peak time Make a circos histogram plot for...

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

Plot histogram for peak time Make a circos histogram plot for peak time.

Description

Plot histogram for peak time Make a circos histogram plot for peak time.

Usage

CP_PlotPeakHist(
  x,
  TOJR = NULL,
  RhyBothOnly = FALSE,
  sig.cut = list(param = "pvalue", fun = "<", val = 0.05),
  time.start = -6,
  Info1 = "groupI",
  Info2 = "groupII",
  GroupSplit = FALSE,
  filename = NULL,
  file.width = 8,
  file.height = 8,
  color.hist = NULL,
  cir.y.breaks = seq(-6, 18, 4),
  single.binwidth = 1,
  axis.text.size = 12,
  legend.position = "right"
)

Arguments

x	CP_Rhythmicity() output
TOJR	toTOJR output. If NULL, rhythm.joint object in x will be used.
RhyBothOnly	For two-group output, plot only RhyBoth genes or all rhythmic genes in separate groups?
sig.cut	A list. Used only for single-group plot, only genes satisfying sig.cut will be plotted. If NULL then genes all genes in regardless of significance in rhythmicity will be plotted. param parameter used for the cutoff. Should be a column in x. fun character string. Either "<", or ">" val numeric. The value used for the cutoff
time.start	numeric. What time do you want the phase start? Default is -6, which is midnight if time is in ZT scale.
Info1	character string. Used in the plot title for group I
Info2	character string. Used in the plot title for group II (if exist).
GroupSplit	logical. For two-group output, should the histogram of each group be plotted separately?
filename	character string. The filename for plot export. If NULL, the plot will not be saved.
file.width	width of the export plot
file.height	height of the export plot
color.hist	Input color. The length of the vector should be the same of the number of the groups.
cir.y.breaks	numeric. A vector for breaks for the angles. Should start with phase.start and end with phase.start+period
single.binwidth	numeric. The binwidth for plotting peak histogram.
axis.text.size	Size for the axis text.
legend.position	One of "left”, "top", "right", "bottom", or "none"

Examples

x = CP_sim_data(ngene=1000, nsample=30, A1=c(2, 3), A2=c(2, 3),
phase1=c(0, pi/4), phase2=c(pi/2, pi*3/2),
M1=c(4, 6), M2=c(4, 6), sigma1=1, sigma2=1)
rhythm.res = CircadianPipeline::CP_Rhythmicity(x1 = x[[1]], x2 = x[[2]])
# Make a two-group plot:
CP_PlotPeakHist(rhythm.res)
# Make a one-group plot
CP_PlotPeakHist(rhythm.res$x1)

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