mp_cal_clust {MicrobiotaProcess} | R Documentation |
Hierarchical cluster analysis for the samples with MPSE or tbl_mpse object
mp_cal_clust( .data, .abundance, distmethod = "bray", hclustmethod = "average", action = "get", ... ) ## S4 method for signature 'MPSE' mp_cal_clust( .data, .abundance, distmethod = "bray", hclustmethod = "average", action = "get", ... ) ## S4 method for signature 'tbl_mpse' mp_cal_clust( .data, .abundance, distmethod = "bray", hclustmethod = "average", action = "get", ... ) ## S4 method for signature 'grouped_df_mpse' mp_cal_clust( .data, .abundance, distmethod = "bray", hclustmethod = "average", action = "get", ... )
.data |
the MPSE or tbl_mpse object |
.abundance |
the name of abundance to be calculated. |
distmethod |
the method of distance. |
hclustmethod |
the method of hierarchical cluster |
action |
a character "add" will return a MPSE object with the cluster result as a attributes, and it can be extracted with 'object "only" or "get" will return 'treedata' object, default is 'get'. |
... |
additional parameters |
update object with the action argument, the treedata object contained hierarchical cluster analysis of sample, it can be visualized with 'ggtree' directly.
Shuangbin Xu
library(ggtree) library(ggplot2) data(mouse.time.mpse) res <- mouse.time.mpse %>% mp_decostand(.abundance=Abundance) %>% mp_cal_clust(.abundance=hellinger, distmethod="bray") res res %>% ggtree() + geom_tippoint(aes(color=time))