mp_cal_pcoa {MicrobiotaProcess} | R Documentation |
Principal Coordinate Analysis with MPSE or tbl_mpse object
mp_cal_pcoa( .data, .abundance, distmethod = "bray", .dim = 3, action = "add", ... ) ## S4 method for signature 'MPSE' mp_cal_pcoa( .data, .abundance, distmethod = "bray", .dim = 3, action = "add", ... ) ## S4 method for signature 'tbl_mpse' mp_cal_pcoa( .data, .abundance, distmethod = "bray", .dim = 3, action = "add", ... ) ## S4 method for signature 'grouped_df_mpse' mp_cal_pcoa( .data, .abundance, distmethod = "bray", .dim = 3, action = "add", ... )
.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 3. |
action |
character "add" joins the pca result to the object and the 'pcoa' object also was add to the internal attributes of the object, "only" return a non-redundant tibble with the pca result. "get" return 'pcoa' object. |
... |
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) mpse mpse %<>% mp_cal_pcoa(.abundance=hellinger, stmethod="bray", action="add") library(ggplot2) p <- mpse %>% mp_plot_ord(.ord=pcoa, .group=time, .color=time, ellipse=TRUE) p <- p + scale_fill_manual(values=c("#00AED7", "#009E73")) + scale_color_manual(values=c("#00AED7", "#009E73")) ## Not run: # Or run with action='only' and return tbl_df to visualize manual. mouse.time.mpse %>% mp_decostand(.abundance=Abundance) %>% mp_cal_pcoa(.abundance=hellinger, distmethod="bray", .dim=2, action="only") -> tbl tbl x <- names(tbl)[grepl("PCo1 ", names(tbl))] %>% as.symbol() y <- names(tbl)[grepl("PCo2 ", names(tbl))] %>% as.symbol() library(ggplot2) tbl %>% ggplot(aes(x=!!x, y=!!y, color=time)) + stat_ellipse(aes(fill=time), geom="polygon", alpha=0.5) + 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)