PlotTimeCourse: PlotTimeCourse

In stefanavey/aveytoolkit: Toolkit of Helper Functions

Description

Plot helper function for PlotPCATimeCourse

Usage

PlotTimeCourse(
  x,
  y,
  colors,
  groups,
  sampleNames,
  pch = 19,
  plotTitle = "",
  legend.loc = "topleft",
  plotType = c("times", "points"),
  alpha = 0.15,
  cex.pt = 1,
  cex.time = 2,
  time.adj = c(-0.3, -0.3),
  arrLen = 0.1,
  lwd = 3,
  numRep = 3,
  plotFont = NULL,
  ctrl = TRUE,
  hourMarks = TRUE,
  legend.cex = 2,
  ...
)

Arguments

x	x-values for plotting
y	y-values for plotting
colors	named vector specifying colors for each sample
groups	the virus strain names for the conditions of interest
sampleNames	names of the samples
pch	the plotting character. Default is 19 (a closed circle).
plotTitle	a string used for the plotting title
legend.loc	location of the legend. Default is topleft.
plotType	one of "times" or "points". See Details
alpha	transparency factor passed to the alpha function (scales library)
cex.pt	size of points. Default is 1
cex.time	size of time labels. Default is 2
time.adj	the ammount to adjust the time labels. Default is c(-.3, -.3) which moves them to the lower left
arrLen	length of the arrows plotted at the average of each time point. Default is 0.1
lwd	line width. Default is 3
numRep	the number of replicates. Default is 3
plotFont	which font to use for plotting text
ctrl	should the control time points be included?
hourMarks	should the 4 and 8 hour time points be marked on the plot?
legend.cex	size expansion for the legened. Default is 2.
...	other arguments passed to heatmap.2

Details

If plotType is "times", ??? Also used to plot 2 genes expression against each other over time. If legend.loc is "none", no legend is plotted. ctrl flag indicates whether or not first numRep values in x and y are from a control measurement

Value

Nothing is returned

Note

Colors are assumed to have as the names attribute some part of the sampleName which can uniquely identify it.

Author(s)

Stefan Avey

stefanavey/aveytoolkit documentation built on March 5, 2020, 12:49 a.m.