viewPlate: View Plate

Description Usage Arguments Author(s) Examples

View source: R/platereader.R

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

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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)

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

Author(s)

Rainer Machne [email protected]

Examples

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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 Nov. 9, 2018, 5:38 p.m.