mp_cal_rarecurve {MicrobiotaProcess} | R Documentation |
Calculating the different alpha diversities index with different depth
mp_cal_rarecurve( .data, .abundance = NULL, action = "add", chunks = 400, seed = 123, force = FALSE, ... ) ## S4 method for signature 'MPSE' mp_cal_rarecurve( .data, .abundance = NULL, action = "add", chunks = 400, seed = 123, force = FALSE, ... ) ## S4 method for signature 'tbl_mpse' mp_cal_rarecurve( .data, .abundance = NULL, action = "add", chunks = 400, seed = 123, force = FALSE, ... ) ## S4 method for signature 'grouped_df_mpse' mp_cal_rarecurve( .data, .abundance = NULL, action = "add", chunks = 400, seed = 123, force = FALSE, ... )
.data |
MPSE or tbl_mpse object |
.abundance |
the name of otu abundance to be calculated. |
action |
character it has three options, "add" joins the new information to the input tbl (default), "only" return a non-redundant tibble with the just new information, ang 'get' return a 'rarecurve' object. |
chunks |
numeric the split number of each sample to calculate alpha diversity, default is 400. eg. A sample has total 40000 reads, if chunks is 400, it will be split to 100 sub-samples (100, 200, 300,..., 40000), then alpha diversity index was calculated based on the sub-samples. |
seed |
a random seed to make the result reproducible, default is 123. |
force |
logical whether calculate rarecurve forcibly when the '.abundance' is not be rarefied, default is FALSE |
... |
additional parameters. |
update rarecurce calss
Shuangbin Xu
[mp_plot_rarecurve()] and [mp_extract_rarecurve()]
data(mouse.time.mpse) mouse.time.mpse %>% mp_rrarefy() -> mpse mpse # larger 'chunks' means more robust, but it will become slower. mpse %<>% mp_cal_rarecurve(.abundance=RareAbundance, chunks=100, action="add") mpse p1 <- mpse %>% mp_plot_rarecurve(.rare=RareAbundanceRarecurve, .alpha="Observe") p2 <- mpse %>% mp_plot_rarecurve(.rare=RareAbundanceRarecurve, .alpha=c("Observe", "ACE"))