mp_balance_clade {MicrobiotaProcess} | R Documentation |
Calculating the balance score of internal nodes (clade) according to the mean/median abundance of their binary children tips.
mp_balance_clade( .data, .abundance = NULL, force = FALSE, relative = TRUE, balance_fun = c("geometric.mean", "mean", "median"), pseudonum = 0.001, action = "get", ... ) ## S4 method for signature 'MPSE' mp_balance_clade( .data, .abundance = NULL, force = FALSE, relative = TRUE, balance_fun = c("geometric.mean", "mean", "median"), pseudonum = 0.001, action = "get", ... ) ## S4 method for signature 'tbl_mpse' mp_balance_clade( .data, .abundance = NULL, force = FALSE, relative = TRUE, balance_fun = c("geometric.mean", "mean", "median"), pseudonum = 0.001, action = "get", ... ) ## S4 method for signature 'grouped_df_mpse' mp_balance_clade( .data, .abundance = NULL, force = FALSE, relative = TRUE, balance_fun = c("geometric.mean", "mean", "median"), pseudonum = 0.001, action = "get", ... )
.data |
MPSE object which must contain otutree slot, required |
.abundance |
the column names of abundance. |
force |
logical whether calculate the (relative) abundance forcibly when the abundance is not be rarefied, default is FALSE. |
relative |
logical whether calculate the relative abundance. |
balance_fun |
function the method to calculate the (relative) abundance of internal nodes according to their children tips, default is 'geometric.mean', other options are 'mean' and 'median'. |
pseudonum |
numeric add a pseudo numeric to avoid the error of division in calculation, default is 0.001 . |
action |
character, "add" joins the new information to the otutree slot if it exists (default). In addition, "only" return a non-redundant tibble with the just new information. "get" return a new 'MPSE' object, and the 'OTU' column is the internal nodes and 'Abundance' column is the balance scores. |
... |
additional parameters, meaningless now. |
a object according to 'action' argument.
Morton JT, Sanders J, Quinn RA, McDonald D, Gonzalez A, Vázquez-Baeza Y, Navas-Molina JA, Song SJ, Metcalf JL, Hyde ER, Lladser M, Dorrestein PC, Knight R. 2017. Balance trees reveal microbial niche differentiation. mSystems 2:e00162-16. https://doi.org/10.1128/mSystems.00162-16.
Justin D Silverman, Alex D Washburne, Sayan Mukherjee, Lawrence A David. A phylogenetic transform enhances analysis of compositional microbiota data. eLife 2017;6:e21887. https://doi.org/10.7554/eLife.21887.001.
## Not run: suppressPackageStartupMessages(library(curatedMetagenomicData)) xx <- curatedMetagenomicData('ZellerG_2014.relative_abundance', dryrun=F) xx[[1]] %>% as.mpse -> mpse mpse.balance.clade <- mpse %>% mp_balance_clade( .abundance = Abundance, force = TRUE, relative = FALSE, action = 'get', pseudonum = .01 ) mpse.balance.clade # Performing the Euclidean distance or PCA. mpse.balance.clade %>% mp_cal_dist(.abundance = Abundance, distmethod = 'euclidean') %>% mp_plot_dist(.distmethod = 'euclidean', .group = disease, group.test = T) mpse.balance.clade %>% mp_adonis(.abundance = Abundance, distmethod = 'euclidean', permutation = 9999) mpse.balance.clade %>% mp_cal_pca(.abundance = Abundance) %>% mp_plot_ord(.group = disease) # Detecting the signal balance nodes. mpse.balance.clade %>% mp_diff_analysis( .abundance = Abundance, force = TRUE, relative = FALSE, .group = disease, fc.method = 'compare_mean' ) ## End(Not run)