mp_cal_upset {MicrobiotaProcess} | R Documentation |
Calculating the samples or groups for each OTU, the result can be visualized by 'ggupset'
mp_cal_upset( .data, .group, .abundance = NULL, action = "add", force = FALSE, ... ) ## S4 method for signature 'MPSE' mp_cal_upset( .data, .group, .abundance = NULL, action = "add", force = FALSE, ... ) ## S4 method for signature 'tbl_mpse' mp_cal_upset( .data, .group, .abundance = NULL, action = "add", force = FALSE, ... ) ## S4 method for signature 'grouped_df_mpse' mp_cal_upset( .data, .group, .abundance = NULL, action = "add", force = FALSE, ... )
.data |
MPSE or tbl_mpse object |
.group |
the name of group to be calculated. if it is no provided, the sample will be used. |
.abundance |
the name of otu abundance to be calculated. if it is null, the rarefied abundance will be used. |
action |
character, "add" joins the new information to the tibble of tbl_mpse or rowData of MPSE. "only" and "get" return a non-redundant tibble with the just new information. which is a treedata object. |
force |
logical whether calculate the relative abundance forcibly when the abundance is not be rarefied, default is FALSE. |
... |
additional parameters. |
update object or tibble according the 'action'
Shuangbin Xu
[mp_plot_upset()]
data(mouse.time.mpse) mpse <- mouse.time.mpse %>% mp_rrarefy() %>% mp_cal_upset(.abundance=RareAbundance, .group=time, action="add") mpse library(ggplot2) library(ggupset) p <- mpse %>% mp_plot_upset(.group=time, .upset=ggupsetOftime) p # or set action="only" ## Not run: tbl <- mouse.time.mpse %>% mp_rrarefy() %>% mp_cal_upset(.abundance=RareAbundance, .group=time, action="only") tbl p2 <- tbl %>% ggplot(aes(x=ggupsetOftime)) + geom_bar() + ggupset::scale_x_upset() + ggupset::theme_combmatrix(combmatrix.label.extra_spacing=30) ## End(Not run)