viewPlate: View Plate

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

Description

plots all data in plate format for a quick inspection of the current data set. This function should be called immediately after loading a new platereader dataset to inspect the data and decide on further processing steps.

Usage

viewPlate(
  data,
  wells,
  wcols,
  rows = toupper(letters[1:8]),
  cols = 1:12,
  xid,
  xscale = FALSE,
  xlim,
  yids,
  dtype = "data",
  pcols,
  yscale = TRUE,
  ylims,
  ylim,
  log = "",
  axes,
  yaxis = "",
  legpos = "topleft",
  add.legend = TRUE,
  verb = FALSE
)

Arguments

data	the list of measurement data as provided by readPlateData
wells	a list of wells to plot, overrules rows and cols
wcols	named color vector for wells, names should correspond to column IDs in data, ie. the column 'well' in the plate layout map
rows	a list of strings/characters used as row ID in the composite row:col well description in the plate layout (map) and plate data
cols	as rows but plate column IDs
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
yids	IDs of the data to be plotted; if missing, all data will be plotted
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.)
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
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
axes	axes numbers to draw, integers from 1 to 4 indicate the side to plot (argument side in function axis); multiple y-axis values (multiple yids) are handled in argumentyaxis
yaxis	the ID of maximally two data types for which y-axes are to be plotted
legpos	position of the well IDs on the plots
add.legend	add a legend for the plotted data types (see argument yids) in the last plotted well
verb	print progress messages

Author(s)

Rainer Machne [e-mail]

Examples

data(ap12)
# view all data on the plate
viewPlate(ap12data)
# inspect natural logarithm of OD_600 values, ie. log(X(t))
viewPlate(ap12data, yids="600", log="y")

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