importExcel: Imports an Excel imaging file and allows some renaming of...

In growthPheno: Functional Analysis of Phenotypic Growth Data to Smooth and Extract Traits

Imports an Excel imaging file and allows some renaming of variables

Description

Uses readxl to import a sheet of imaging data produced by the Lemna Tec Scanalyzer. Basically, the data consists of imaging data obtained from a set of pots or carts over time. There should be a column, which by default is called Snapshot.ID.Tag, containing a unique identifier for each cart and a column, which by default is labelled Snapshot.Time.Stamp, containing the time of imaging for each observation in a row of the sheet. Also, if startTime is not NULL, calcTimes is called to calculate, or recalculate if already present, timeAfterStart from imageTimes by subtracting a supplied startTime.

Using cameraType, keepCameraType, labsCamerasViews and prefix2suffix, some flexibility is provided for renaming the columns with imaging data. For example, if the column names are prefixed with 'RGB_SV1', 'RGB_SV2' or 'RGB_TV', the 'RGB_' can be removed and the 'SV1', 'SV2' or 'TV' become suffices.

Usage

importExcel(file, sheet="raw data", sep = ",", 
            cartId = "Snapshot.ID.Tag", 
            imageTimes = "Snapshot.Time.Stamp", 
            timeAfterStart = "Time.after.Planting..d.", 
            cameraType = "RGB", keepCameraType = FALSE, 
            labsCamerasViews = NULL, prefix2suffix = TRUE, 
            startTime = NULL,
            timeFormat = "%Y-%m-%d %H:%M", 
            plotImagetimes = TRUE, ...)

Arguments

file	A character giving the path and name of the file containing the data.
sheet	A character giving the name of the sheet containing the data, that must include columns whose names are as specified by cartId, which uniquely indexes the carts in the experiment, and imageTimes, which reflects the time of the imaging from which a particular data value was obtained. It is also assumed that a column whose name is specified by timeAfterStart is in the sheet or that it will be calculated from imageTimes using the value of startTime supplied in the function call.
sep	A character giving the separator used in a csv file.
cartId	A character giving the name of the column that contains the unique Id for each cart. Note that in importing data into R, spaces and nonalphanumeric characters in names are converted to full stops.
imageTimes	A character giving the name of the column that contains the time that each cart was imaged. Note that in importing data into R, spaces and nonalphanumeric characters in names are converted to full stops.
timeAfterStart	A character giving the name of the column that contains or is to contain the difference between imageTimes and startTime. The function calcTimes is called to calculate the differences. For example, it might contain the number of days after planting. Note that in importing data into R, spaces and nonalphanumeric characters in names are converted to full stops.
cameraType	A character string nominating the abbreviation used for the cameraType. A warning will be given if no variable names include this cameraType.
keepCameraType	A logical specifying whether to retain the cameraType in the variables names. It will be the start of the prefix or suffix and separated from the remander of the prefix or suffix by an underscore (_).
labsCamerasViews	A named character whose elements are new labels for the camera-view combinations and the name of each element is the old label for the camera-view combination in the data being imported. If labsCamerasViews is NULL, all column names beginning with cameraType are classed as imaging variables and the unique prefixes amongst them determined. If no imaging variables are found then no changes are made. Note that if you want to include a recognisable cameraType in a camier-view label, it should be at the start of the the label in labsCamerasViews and separated from the rest of the label by an underscore (_).
prefix2suffix	A logical specifying whether the variables names with prefixed camera-view labels are to have those prefixes transferred to become suffices. The prefix is assumed to be all the characters up to the first full stop (.) in the variable name and must contain cameraType to be moved. It is generally assumed that the characters up to the first underscore (_) are the camera type and this is removed if keepCameraType is FALSE. If there is no underscore (_), the whole prefix is moved. If labsCamerasViews is NULL, all column names beginning with cameraType are classed as imaging variables and the unique prefixes amongst them determined. If no imaging variables are found then no changes are made.
startTime	A character giving the time of planting, in the POSIXct format timeFormat, to be subtracted from imageTimes in recalculating timeAfterStart. If startTime is NULL then timeAfterStart is not recalculated.
timeFormat	A character giving the POSIXct format of characters containing times, in particular imageTimes and startTime.
plotImagetimes	A logical indicating whether a plot of the imaging times against the recalculated Time.After.Planting..d.. It aids in checking Time.After.Planting..d. and what occurred in imaging the plants.
...	allows for arguments to be passed to plotImagetimes. However, if intervals is passed an error will occur; use timeAfterStart instead.

Value

A data.frame containing the data.

Author(s)

Chris Brien

See Also

as.POSIXct, calcTimes, plotImagetimes

Examples

filename <- system.file("extdata/rawdata.xlsx", package = "growthPheno", 
                        mustWork = TRUE)
raw.dat <- importExcel(file = filename, 
                       startTime  = "2015-02-11 0:00 AM")


camview.labels <- c("SF0", "SL0", "SU0", "TV0")
names(camview.labels) <- c("RGB_Side_Far_0", "RGB_Side_Lower_0", 
                           "RGB_Side_Upper_0", "RGB_TV_0")
filename <- system.file("extdata/raw19datarow.csv", package = "growthPheno", 
                        mustWork = TRUE)
raw.19.dat <- suppressWarnings(importExcel(file = filename,
                                           cartId = "Snapshot.ID.Tags",
                                           startTime = "06/10/2017 0:00 AM",
                                           timeFormat = "%d/%m/%Y %H:M", 
                                           labsCamerasViews = camview.labels, 
                                           plotImagetimes = FALSE))

growthPheno documentation built on Sept. 11, 2024, 6:42 p.m.