viewGroups: View Group Averages

In raim/platexpress: Inspection and Analysis of Microbial Growth and Gene Expression Data

Description

plot grouped wells as summary plots, incl. means and confidence intervals. This function gives a first overview of the reproducability between replicates.

Usage

viewGroups(
  data,
  yids,
  stats = "CI",
  groups,
  groups2,
  xid,
  xscale = FALSE,
  xlim,
  xlab,
  dtype = "data",
  ylab,
  pcols,
  group2.col,
  yscale = TRUE,
  ylims,
  ylim,
  log = "",
  lty.mean = 1,
  lwd.mean = 2,
  alpha = 55,
  lty.orig = 1,
  lwd.orig = 0.1,
  show.ci95 = FALSE,
  show.mean = TRUE,
  emphasize.mean = FALSE,
  g2.legpos = "topleft",
  g2.legend = TRUE,
  embed = FALSE,
  no.par = FALSE,
  mai = c(0.5, 0, 0, 0),
  xmgp = c(1.5, 0.5, 0),
  ymgp = c(0, -1, -0.05),
  ytcl = 0.25,
  nrow = 1,
  xaxis = TRUE,
  yaxis = c(1, 2),
  g1.legpos = "topright",
  g1.legend = TRUE,
  verb = FALSE
)

Arguments

data	the platereader data object as provided by readPlateData
yids	IDs of the data to be plotted; if missing, all data will be plotted
stats	type of replicate statistics to plot, where replicates are defined in option groups2 or defined in the plate data object. Options are either only a line for each replicate group ("mean" or "median") or a line with transparent ranges. "CI": mean and 95% confidence interval (default), "SD": mean and standard deviation, "SE": mean and standard error, "boxplot": median and 25% and 75% quantiles, "range": median and full data range (min/max)
groups	a list of well groups, wells from each group will be plotted together in one plot, and statistics plotted for sub-groups (replicates) in groups2. Groupings can also be present as a list item in the data object.
groups2	replicate well groups for which statistics are calculated and plotted (see argument stats), each group must be a subset of exactly on well group in argument groups.
xid	ID of a data-set in the input data that can be used as x-axis instead of the default Time vector
xscale	use a global range for the x-axes; only relevant if xid specifies a subset of the data as x-axis
xlim	plot range of the x-axis
xlab	custom x-axis label
dtype	type of the data to be plotted, default is the main 'data', but e.g. 'orig' allows to plot the original data w/o processing (e.g. interpolation, blank correction, etc.)
ylab	custom y-axis label
pcols	a named list of RGB colors to be used the plotted data types; the color vector must have names according to the data IDs
group2.col	a named list of RGB colors for group2 (which are shown in one plot)
yscale	if TRUE (default) global y-axis limits will be calculated from all plotted wells; if FALSE each well be locally scaled
ylims	a named list of y-axis ranges pairs for each data ID
ylim	one y-axis limit range that will be used for all plotted data
log	plot logarithmic axis, use equivalent to normal plot 'log', i.e., log="y" for a log y-axis, log="x" for x-axis and log="yx" for both axes
lty.mean	line style for the mean lines, see (par("lty") this can help to emphasize the means in noisy data (broad overlapping confidence intervals
lwd.mean	line width for the mean lines, see (par("lwd")
alpha	hexadecimal alpha value for range plot opaqueness
lty.orig	line type of the original single data, set to 0 to supress plotting of all original data
lwd.orig	line-width of the original single data, set to 0 to supress plotting of all original data
show.ci95	deprecated, but kept for backward compatibility, see option stats="CI": show the 95% condifence intervals of groups; set stats="mean" to reproduce previous show.ci95=FALSE behaviour
show.mean	show the mean of groups as lines
emphasize.mean	show the means in black instead of group colors,
g2.legpos	position of the groups2 legend, see g2.legend
g2.legend	plot a legend for groups in argument groups2
embed	setting TRUE allows to embed plots of single groups within in layouted plots, see ?layout and par("mfcol"); also see argument no.par
no.par	setting TRUE supresses all internal plot defaults (e.g., mai, mgp), useful to style your own plots, also see argument embed
mai	set the outer margins around plot areas, see ?par
xmgp	x-axis mgp settings: margin line in mex units of axis title, tick labels and axis line; used only if no.par==FALSE
ymgp	y-axis mgp settings: margin line in mex units of axis title, tick labels and axis line
ytcl	y-axis tcl settings: tick length and direction
nrow	number of plot rows, number of columns will be selected automatically; NOTE: to change the ordering of the plots you can change the ordering of the input groups/
xaxis	plot x-axis if TRUE
yaxis	the data types for which axes are to be plotted, corresponds to the order in argument yids and as plotted in the legend (see argument g1.legend
g1.legpos	position of the groups legend, see g1.legend
g1.legend	show the main legend, giving plot colors
verb	print progress messages

Author(s)

Rainer Machne [e-mail]

See Also

viewPlate, getGroups, readPlateMap

Examples

data(ap12)
groups <- getGroups(plate=ap12plate, by=c("strain"))
vg <- viewGroups(ap12data,groups=groups,lwd.orig=0.1,nrow=1)
vg <- viewGroups(ap12data,groups2=groups,lwd.orig=0.1,nrow=1)

raim/platexpress documentation built on Jan. 18, 2022, 1:41 p.m.