trans_func {microeco} | R Documentation |
This class is a wrapper for a series of functional analysis on species and communities, including the prokaryotes function identification based on Louca et al. (2016) <doi:10.1126/science.aaf4507> or fungi function identification based on Nguyen et al. (2016) <10.1016/j.funeco.2015.06.006>, functional redundancy calculation and metabolic pathway abundance prediction Aßhauer et al. (2015) <10.1093/bioinformatics/btv287>.
func_group_list
store and show the function group list
new()
trans_func$new(dataset = NULL)
dataset
the object of microtable
Class.
for_what : "prok" or "fungi" or NA, "prok" represent prokaryotes. "fungi" represent fungi. NA represent not identified according to the Kingdom information, at this time, if you want to use the functions to identify species traits, you need provide "prok" or "fungi" manually, e.g. dataset$for_what <- "prok".
data(dataset) t1 <- trans_func$new(dataset = dataset)
cal_spe_func()
Confirm traits of each OTU by matching the taxonomic assignments to the functional database; Prokaryotes: based on the FAPROTAX database, please also cite the original FAPROTAX paper: Louca, S., Parfrey, L. W., & Doebeli, M. (2016). Decoupling function and taxonomy in the global ocean microbiome. Science, 353(6305), 1272. <doi:10.1126/science.aaf4507>; Fungi, based on the FUNGuild database, please also cite: Nguyen, N. H., Song, Z., Bates, S. T., Branco, S., Tedersoo, L., Menke, J., … Kennedy, P. G. (2016). FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecology, 20(1), 241–248. <doi:10.1016/j.funeco.2015.06.006>
trans_func$cal_spe_func()
res_spe_func in object.
\donttest{ t1$cal_spe_func() }
cal_spe_func_perc()
Calculating the percentages of species with specific trait in communities or modules. The percentages of the OTUs with specific trait can reflect the potential of the corresponding function in the community or the module in the network.
trans_func$cal_spe_func_perc( use_community = TRUE, node_type_table = NULL, abundance_weighted = FALSE )
use_community
default TRUE; whether calculate community; if FALSE, use module.
node_type_table
default NULL; If use_community FALSE; provide the node_type_table with the module information, such as the result of cal_node_type.
abundance_weighted
default FALSE; whether use abundance. If FALSE, calculate the functional population percentage. If TRUE, calculate the functional individual percentage.
res_spe_func_perc in object.
\donttest{ t1$cal_spe_func_perc(use_community = TRUE) }
show_prok_func()
Show the basic information for a specific function of prokaryotes.
trans_func$show_prok_func(use_func = NULL)
use_func
default NULL; the function name.
None.
\donttest{ t1$show_prok_func(use_func = "methanotrophy") }
plot_spe_func_perc()
Plot the percentages of species with specific trait in communities or modules.
trans_func$plot_spe_func_perc( filter_func = NULL, use_group_list = TRUE, add_facet = TRUE, select_samples = NULL )
filter_func
default NULL; a vector of function names.
use_group_list
default TRUE; If TRUE, use default group list; If use personalized group list, first set trans_func$func_group_list object with a list of group names and functions.
add_facet
default TRUE; whether use group names as the facets in the plot, see trans_func$func_group_list object.
select_samples
default NULL; character vector, select partial samples to show
ggplot2.
\donttest{ t1$plot_spe_func_perc(use_group_list = TRUE) }
cal_FAPROTAX()
Predict functional potential of communities using FAPROTAX. please also cite the original FAPROTAX paper: Louca, S., Parfrey, L. W., & Doebeli, M. (2016). Decoupling function and taxonomy in the global ocean microbiome. Science, 353(6305), 1272. <doi:10.1126/science.aaf4507>;
trans_func$cal_FAPROTAX(keep_tem = TRUE)
keep_tem
default FALSE; whether keep the intermediate file, that is, the otu_table_for_FAPROTAX.txt in local place.
res_FAPROTAX in object.
\donttest{ t1$cal_FAPROTAX() }
cal_tax4fun()
Predict functional potential of communities using tax4fun. please also cite: Aßhauer, K. P., Wemheuer, B., Daniel, R., & Meinicke, P. (2015). Tax4Fun: Predicting functional profiles from metagenomic 16S rRNA data. Bioinformatics, 31(17), 2882–2884. <doi:10.1093/bioinformatics/btv287>
trans_func$cal_tax4fun(keep_tem = FALSE, folderReferenceData = NULL)
keep_tem
default FALSE; whether keep the intermediate file, that is, the otu table in local place.
folderReferenceData
default NULL; the folder, see http://tax4fun.gobics.de/ and Tax4Fun function in Tax4Fun package.
tax4fun_KO and tax4fun_path in object.
\donttest{ t1$cal_tax4fun(folderReferenceData = "./SILVA123") }
print()
Print the trans_func object.
trans_func$print()
clone()
The objects of this class are cloneable with this method.
trans_func$clone(deep = FALSE)
deep
Whether to make a deep clone.
## ------------------------------------------------ ## Method `trans_func$new` ## ------------------------------------------------ data(dataset) t1 <- trans_func$new(dataset = dataset) ## ------------------------------------------------ ## Method `trans_func$cal_spe_func` ## ------------------------------------------------ t1$cal_spe_func() ## ------------------------------------------------ ## Method `trans_func$cal_spe_func_perc` ## ------------------------------------------------ t1$cal_spe_func_perc(use_community = TRUE) ## ------------------------------------------------ ## Method `trans_func$show_prok_func` ## ------------------------------------------------ t1$show_prok_func(use_func = "methanotrophy") ## ------------------------------------------------ ## Method `trans_func$plot_spe_func_perc` ## ------------------------------------------------ t1$plot_spe_func_perc(use_group_list = TRUE) ## ------------------------------------------------ ## Method `trans_func$cal_FAPROTAX` ## ------------------------------------------------ t1$cal_FAPROTAX() ## ------------------------------------------------ ## Method `trans_func$cal_tax4fun` ## ------------------------------------------------ t1$cal_tax4fun(folderReferenceData = "./SILVA123")