files2SpectraObject: Import Data into a Spectra Object

Description Usage Arguments Value Functions files2SpectraObject matrix2SpectraObject gr.crit and Sample Name Gotchas Author(s) References See Also Examples

View source: R/files2SpectraObject.R

Description

These functions import data into a Spectra object. They use read.table to read files so they are very flexible in regard to file formatting. Be sure to see the ... argument below for important details you need to provide.

Usage

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files2SpectraObject(gr.crit = NULL, gr.cols = c("auto"),
  freq.unit = "no frequency unit provided",
  int.unit = "no intensity unit provided",
  descrip = "no description provided", fileExt = "\\.(csv|CSV)$",
  out.file = "mydata", debug = FALSE, ...)

matrix2SpectraObject(gr.crit = NULL, gr.cols = c("auto"),
  freq.unit = "no frequency unit provided",
  int.unit = "no intensity unit provided",
  descrip = "no description provided", in.file = NULL,
  out.file = "mydata", chk = TRUE, ...)

Arguments

gr.crit

Group Criteria. A vector of character strings which will be searched for among the file/sample names in order to assign an individual spectrum to group membership. This is done using grep, so characters like "." (period/dot) do not have their literal meaning (see below). Warnings are issued if there are file/sample names that don't match entries in gr.crit or there are entries in gr.crit that don't match any file names. A maximum of 8 groups can automatically be assigned colors and symbols. If you have more than 8 groups, you will need to provide a vector of colors (see below) and manually fix the symbols after the Spectra object is created.

gr.cols

Group Colors. Either the word "auto", in which case colors will be automatically assigned, or a vector of acceptable color names with the same length as gr.crit. In the latter case, colors will be assigned one for one, so the first element of gr.crit is assigned the first element of gr.col and so forth. A maximum of 8 colors can be assigned automatically, after that, you must give a vector of colors. See details below for some other issues to consider.

freq.unit

A character string giving the units of the x-axis (frequency or wavelength).

int.unit

A character string giving the units of the y-axis (some sort of intensity).

descrip

A character string describing the data set that will be stored. This string is used in some plots so it is recommended that its length be less than about 40 characters.

fileExt

A character string giving the extension of the files to be processed. regex strings can be used. For instance, the default finds files with either ".csv" or ".CSV" as the extension. Matching is done via a grep process, which is greedy.

out.file

A file name. The completed object of S3 class Spectra will be written to this file.

debug

Logical. Applies to files2SpectraObject only. Set to TRUE for troubleshooting when an error is thrown during import. In addition, values of 1-5 will work when importing a JCAMP-DX file via fileExt = ".jdx" etc. These will be passed through to the readJDX function. See there for much more info on importing JCAMP-DX files.

...

Arguments to be passed to read.table. You MUST supply values for sep, dec and header consistent with your file structure, unless they are the same as the defaults for read.table.

in.file

Character. Applies to matrix2SpectraObject only. Input file name, including extension.

chk

Logical. Applies to matrix2SpectraObject only. Should the Spectra object be checked for integrity? If you are having trouble importing your data, set this to FALSE and do str(your object) to troubleshoot.

Value

A object of class Spectra. An unnamed object of S3 class Spectra is also written to out.file. To read it back into the workspace, use new.name <- loadObject(out.file) (loadObject is package R.utils).

Functions

files2SpectraObject

files2SpectraObject acts on all files in the current working directory with the specified fileExt so there should be no extra files of that type hanging around (except see next paragraph). The first column should contain the frequency values and the second column the intensity values. The files may have a header or not (supply header = TRUE/FALSE as necessary). The frequency column is assumed to be the same in all files.

If fileExt contains any of "dx", "DX", "jdx" or "JDX", then the files will be processed by readJDX. Consider setting debug = TRUE for this format, as there are many options for JCAMP, and many are untested. See readJDX for known limitations.

matrix2SpectraObject

This function takes a csv-like file, containing frequencies in the first column, and samples in additional columns, and processes it into a Spectra object. The file MUST have a header row which includes the sample names. There need not be a header for the first (frequency) column.

gr.crit and Sample Name Gotchas

The matching of gr.crit against the sample file names (in files2SpectraObject) or column headers/sample names (in codematrix2SpectraObject) is done one at a time, in order, using grep. While powerful, this has the potential to lead to some "gotchas" in certain cases, noted below.

Your file system may allow file/sample names which R will not like, and will cause confusing behavior. File/sample names become variables in ChemoSpec, and R does not like things like "-" (minus sign or hyphen) in file/sample names. A hyphen is converted to a period (".") if found, which is fine for a variable name. However, a period in gr.crit is interpreted from the grep point of view, namely a period matches any single character. At this point, things may behave very differently than one might hope. See make.names for allowed characters in R variables and make sure your file/sample names comply.

The entries in gr.crit must be mutually exclusive. For example, if you have files with names like "Control_1" and "Sample_1" and use gr.crit = c("Control", "Sample") groups will be assigned as you would expect. But, if you have file names like "Control_1_Shade" and "Sample_1_Sun" you can't use gr.crit = c("Control", "Sample", "Sun", "Shade") because each criteria is grepped in order, and the "Sun/Shade" phrases, being last, will form the basis for your groups. Because this is a grep process, you can get around this by using regular expressions in your gr.crit argument to specify the desired groups in a mutually exclusive manner. In this second example, you could use gr.crit = c("Control(.*)Sun", "Control(.*)Shade", "Sample(.*)Sun", "Sample(.*)Shade") to have your groups assigned based upon both phrases in the file names.

To summarize, gr.crit is used as a grep pattern, and the file/sample names are the target. Make sure your file/sample names comply with make.names.

Finally, samples whose names are not matched using gr.crit are still incorporated into the Spectra object, but they are not assigned a group or color. Therefore they don't plot, but they do take up space in a plot! A warning is issued in these cases, since one wouldn't normally want a spectrum to be orphaned this way.

All these problems can generally be identified by running sumSpectra once the data is imported.

Author(s)

Bryan A. Hanson, DePauw University.

References

https://github.com/bryanhanson/ChemoSpec

See Also

The linking of groups with colors is handled by groupNcolor.

Examples

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# Grab an included file
ed <- system.file("extdata", package = "ChemoSpec")
tf <- "PCRF.jdx"
chk <- file.copy(from = file.path(ed, tf), to = file.path(getwd(), tf),
	overwrite = TRUE)

# Now read in the file, and plot
spec <- files2SpectraObject(gr.crit = "PCRF", freq.unit = "ppm", int.unit = "intensity",
  descrip = "test import", fileExt = ".jdx")
sumSpectra(spec)
plotSpectra(spec, lab.pos = 3.5, main = "Reduced Fat Potato Chip")

ChemoSpec documentation built on Dec. 13, 2017, 1:07 a.m.