CP_PlotPeakDiff: Circos plot for peak time shift Make a circos plot for peak...

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

Circos plot for peak time shift Make a circos plot for peak time shift between two groups

Description

Circos plot for peak time shift Make a circos plot for peak time shift between two groups

Usage

CP_PlotPeakDiff(
  x,
  TOJR,
  dPhase,
  color.cut = list(param = "pvalue", fun = "<", val = 0.05, color.sig = "#b33515",
    color.none = "dark grey"),
  color.df = NULL,
  Info1 = "groupI",
  Info2 = "groupII",
  filename = NULL,
  file.width = 8,
  file.height = 8,
  time.start = -6,
  concordance.ref = 4,
  cir.x.breaks = seq(-12, 12, 4),
  cir.y.breaks = seq(-6, 18, 4),
  axis.text.size = 12,
  legend.position = "right",
  color.diff.refband = "darkgreen",
  color.diff.connectline = "grey80",
  color.diff.baseline = "blue"
)

Arguments

x	CP_Rhythmicity() output.
TOJR	toTOJR output. If NULL, rhythm.joint object in x will be used.
dPhase	CP_DiffPar() output with phase shift tested.
color.cut	list. Genes will be plotted according a cutoff. Used only when dPhase is not NULL. param parameter used for the cutoff. Should be a column in dPhase. fun character string. Either "<", or ">" val numeric. The value used for the cutoff. color.sig color for points that pass the color.cut criterion. color.none color for points that do not pass the color.cut criterion.
color.df	data.frame. A more advanced color coding. The data frame should have two columns named color and label. label will be displayed as legend. The color vector should have the same order as genes in dPhase.
Info1	character string. Used in the plot title for group I
Info2	character string. Used in the plot title for group II (if exist).
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
time.start	numeric. What time do you want the phase start? Default is -6, which is midnight if time is in ZT scale.
concordance.ref	The radius where the concordance reference line be plotted away from Δpeak = 0.
cir.x.breaks	numeric. A vector for breaks for the radius (peak difference). Should only contains values from -period/2 to period/2 and it is recommended that the break is equal spaced.
cir.y.breaks	numeric. A vector for breaks for the angles. Should start with time.start and end with time.start+period
axis.text.size	numeric. Size for the axis text.
legend.position	One of "left”, "top", "right", "bottom", or "none"
color.diff.refband	color of the reference band around Δpeak = 0.
color.diff.connectline	color of the start and end of the peak difference range.
color.diff.baseline	color of the reference line for Δpeak = 0.

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]])
rhythm.diffPar = CircadianPipeline::CP_DiffPar(rhythm.res, "phase")
#make a plot with genes with differential phase p-value<0.05 in a different color
CP_PlotPeakDiff(rhythm.res, NULL, rhythm.diffPar)

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