mp_cal_pca {MicrobiotaProcess} | R Documentation |
Principal Components Analysis with MPSE or tbl_mpse object
mp_cal_pca(.data, .abundance, .dim = 3, action = "add", ...) ## S4 method for signature 'MPSE' mp_cal_pca(.data, .abundance, .dim = 3, action = "add", ...) ## S4 method for signature 'tbl_mpse' mp_cal_pca(.data, .abundance, .dim = 3, action = "add", ...) ## S4 method for signature 'grouped_df_mpse' mp_cal_pca(.data, .abundance, .dim = 3, action = "add", ...)
.data |
MPSE or tbl_mpse object |
.abundance |
the name of abundance to be calculated. |
.dim |
integer The number of dimensions to be returned, default is 3. |
action |
character "add" joins the pca result to the object, "only" return a non-redundant tibble with the pca result. "get" return 'prcomp' object. |
... |
additional parameters see also 'prcomp' |
update object or tbl according to the action.
Shuangbin Xu
data(mouse.time.mpse) library(ggplot2) mpse <- mouse.time.mpse %>% mp_decostand(.abundance=Abundance) %>% mp_cal_pca(.abundance=hellinger, action="add") mpse p1 <- mpse %>% mp_plot_ord(.ord=pca, .group=time, ellipse=TRUE) p2 <- mpse %>% mp_plot_ord(.ord=pca, .group=time, .color=time, ellipse=TRUE) p1 + scale_fill_manual(values=c("#00AED7", "#009E73")) p2 + scale_fill_manual(values=c("#00AED7", "#009E73")) + scale_color_manual(values=c("#00AED7", "#009E73")) ## Not run: # action = "only" to extract the non-redundant tibble to visualize tbl <- mouse.time.mpse %>% mp_decostand(.abundance=Abundance) %>% mp_cal_pca(.abundance=hellinger, action="only") tbl x <- names(tbl)[grepl("PC1 ", names(tbl))] %>% as.symbol() y <- names(tbl)[grepl("PC2 ", names(tbl))] %>% as.symbol() ggplot(tbl) + geom_point(aes(x=!!x, y=!!y, color=time)) ## End(Not run)