mp_cal_venn {MicrobiotaProcess} | R Documentation |
Calculating the OTU for each sample or group, the result can be visualized by 'ggVennDiagram'
mp_cal_venn( .data, .group, .abundance = NULL, action = "add", force = FALSE, ... ) ## S4 method for signature 'MPSE' mp_cal_venn( .data, .group, .abundance = NULL, action = "add", force = FALSE, ... ) ## S4 method for signature 'tbl_mpse' mp_cal_venn( .data, .group, .abundance = NULL, action = "add", force = FALSE, ... ) ## S4 method for signature 'grouped_df_mpse' mp_cal_venn( .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. |
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_venn()]
data(mouse.time.mpse) mouse.time.mpse %>% mp_rrarefy() %>% mp_cal_venn(.abundance=RareAbundance, .group=time, action="add") -> mpse mpse p <- mpse %>% mp_plot_venn(.venn = vennOftime, .group = time) ## Not run: # visualized by manual library(ggplot2) mpse %>% mp_extract_sample() %>% select(time, vennOftime) %>% distinct() %>% pull(var=vennOftime, name=time) %>% ggVennDiagram::ggVennDiagram() ## End(Not run)