jonesDatum-class: Jones Datum object

In Khlick/jonesDataClass: Class Objects To Manage Calcium Imaging Data From Dr. Jones

Description

Jones Datum object

plot

subset

Usage

## S4 method for signature 'jonesDatum,character'
plot(x, y = c("raw", "adjusted",
  "standardized", "background", "corrected"), xlab = "", ylab = "",
  axes = FALSE, ...)

## S4 method for signature 'jonesDatum'
subset(x, subset, select, type = c("adjusted", "raw",
  "standardized", "background", "corrected"), drop = FALSE, ...)

Arguments

x	jonesDatum object, required
y	char of: 'raw', 'adjusted', 'scaled', 'background', 'corrected'
xlab	X-axis label (units will be appended)
ylab	Y-axis label (units will be appended)
axes	bool, draw with or without axes (FALSE by default)
...	for plot: passed to plot.window. otherwise unused.
subset	logical test for rows
select	logical test for columns
type	type=c('adjusted', 'standardized','raw','background','corrected')
drop	sent to indexing operation for x[,,drop]

Fields

fileName

Provide the full path to teh file

metaData

no input. contains metadata and info for file

data

no input. list of data types: Raw, Adjusted, Rescaled and Time vector

background

no input. contains, if applicable, lum, roi and area of background roi

ares

no input. data.frame of cell# and corresponding roi area

rois

no input. named list for each roi in the dataset

image

no input. Contains the image data, if applicable.

Methods

getConfluence()

Report confluence as a percent (0-100).

getData(type = c("adjusted", "standardized", "raw", "background", "corrected"))

Extract full dataset of provided type.

getDataAsList(type = c("adjusted", "standardized", "raw", "background", "corected"))

Extract the data as a named list of X,Y datasets for each Cell.

getIDs()

Get the names of the cell IDs

getOtherTreatment()

Check the other treatments, typically IL-1b.

getTreatment()

Report Treatment type, typically ET1.

isConfluent(prcnt = 100)

Check if confluence is == prcnt.

isET1()

Check if ET1 is in the primary treatment.

isIL1b()

Check if IL1b is in other treatments.

plotImage(channel = c("green", "all", "red", "blue"), ofst = 0, greyscale = FALSE, equalize = TRUE, gamma = 2.2, colors = NULL, texts = NULL, draw.roi = TRUE, roi.alpha = 0.5, draw.text = TRUE, text.color = NULL, ...)

Plots the corresponding image if applicable.
channel: Choose a specific channel or 'all' for all channels.
ofst: Value to set unchosen channels on [0,1] can reduce contrast
greyscale: boolean, convert image to greyscale (2d indexed)
equalize: boolean, Use histogram equalization
gamma: double, used if greyscale or hist equalization
colors: hex color matrix for ROIs (defaults to all red)
draw.roi boolean, Draw the ROIs over the image
roi.alpha double, Transparency level for ROI on [0,1]
draw.text boolean, Draw text labels, provided or otheriwse, at the centroid of each ROI
text.color array, Hex color vector. If scalar, color is applied to all text, otherwise it must be the same length as .self$nCells().
...: Parameters passed to plot.window().

save(pathName, objectName = "", ...)

Save the current object on the file in R external object format.

Khlick/jonesDataClass documentation built on May 26, 2019, 4:37 p.m.