mp_cal_nmds {MicrobiotaProcess} | R Documentation |
Nonmetric Multidimensional Scaling Analysis with MPSE or tbl_mpse object
mp_cal_nmds( .data, .abundance, distmethod = "bray", .dim = 2, action = "only", seed = 123, ... ) ## S4 method for signature 'MPSE' mp_cal_nmds( .data, .abundance, distmethod = "bray", .dim = 2, action = "only", seed = 123, ... ) ## S4 method for signature 'tbl_mpse' mp_cal_nmds( .data, .abundance, distmethod = "bray", .dim = 2, action = "only", seed = 123, ... ) ## S4 method for signature 'grouped_df_mpse' mp_cal_nmds( .data, .abundance, distmethod = "bray", .dim = 2, action = "only", seed = 123, ... )
.data |
MPSE or tbl_mpse object |
.abundance |
the name of abundance to be calculated. |
distmethod |
character the method to calculate distance. |
.dim |
integer The number of dimensions to be returned, default is 2. |
action |
character "add" joins the NMDS result to the object, "only" return a non-redundant tibble with the NMDS result. "get" return 'metaMDS' object can be analyzed with related 'vegan' function. |
seed |
a random seed to make this analysis reproducible, default is 123. |
... |
additional parameters see also 'mp_cal_dist'. |
update object or tbl according to the action.
Shuangbin Xu
data(mouse.time.mpse) mpse <- mouse.time.mpse %>% mp_decostand(.abundance=Abundance) %>% mp_cal_nmds(.abundance=hellinger, distmethod="bray", action="add") library(ggplot2) p <- mpse %>% mp_plot_ord(.ord=nmds, .group=time, .color=time, .alpha=0.8, ellipse=TRUE, show.sample=TRUE) p <- p + scale_fill_manual(values=c("#00AED7", "#009E73")) + scale_color_manual(values=c("#00AED7", "#009E73")) ## Not run: mouse.time.mpse %>% mp_decostand(.abundance=Abundance) %>% mp_cal_nmds(.abundance=hellinger, distmethod="bray", .dim=2, action="only") -> tbl tbl x <- names(tbl)[grepl("NMDS1", names(tbl))] %>% as.symbol() y <- names(tbl)[grepl("NMDS2", names(tbl))] %>% as.symbol() library(ggplot2) tbl %>% ggplot(aes(x=!!x, y=!!y, color=time)) + geom_point() + geom_vline(xintercept=0, color="grey20", linetype=2) + geom_hline(yintercept=0, color="grey20", linetype=2) + theme_bw() + theme(panel.grid=element_blank()) ## End(Not run)