Spectra object. The file should contain a header row which includes the sample names. The file can have any combination of delimiters and decimal marks (see below).
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, ...)gr.crit or there are entries in gr.crit that don't match any file names. See Details for some nuances.
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. See details below for some other issues to consider.
save function. The completed object of S3 class Spectra will be written to this file.
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.
read.table. In particular, you MUST give a value for sep and decimal, nothing is assumed. This gives maximum flexibility in reading in a variety of formats.
Spectra object, but they are not assigned a group or color and therefore don't plot, but they do take up space in a plot!groupNcolor.
The matching of gr.crit against the sample file names is done one at a time, in order. This means that 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.