Exports EEMs contour plots to a file
plot_eems.RdWill plot EEMs using 'ggeem2' function then will export plots to specified file.
Usage
plot_eems(
prjpath,
meta,
eem,
sing_plot = T,
sum_plot = T,
doc_norm = T,
ncol = 4,
title = "description",
save_names = "",
...
)Arguments
- prjpath
a string indicating the project file
- meta
the metadata associated with the samples
- eem
object of class eemlist with EEMs to be plotted
- sing_plot
logical, if TRUE will create and save a separate plot for each EEMs
- sum_plot
logical, if TRUE will create and save a plot with all the EEMs in a single plot
- doc_norm
either TRUE, FALSE. TRUE return EEMs normalized by DOC concentration
- ncol
number of columns used in summary plot with all the EEMs samples
- title
either a dataframe with samples and titles, 'description', 'sampleID', or FALSE (see details)
- save_names
optional, a character that will be added to the unique ID for plot file names
- ...
arguments to pass to 'ggeems2' function
Details
Use 'create_files' function before running this function to ensure file structure is correct for pre-processing.
For title argument, you can specify the title manually, by using a dataframe where the first column in the unique ID's for the samples and the second column is the title. If 'description' is chosen it will use the description column of the metadata. If 'sampleID' is chosen it will use the unique identifier column from the metadata. Lastly if FALSE is chosen no titles will be added.