mp_plot_rarecurve {MicrobiotaProcess} | R Documentation |
Rarefaction alpha index with MPSE
mp_plot_rarecurve( .data, .rare, .alpha = c("Observe", "Chao1", "ACE"), .group = NULL, nrow = 1, plot.group = FALSE, ... ) ## S4 method for signature 'MPSE' mp_plot_rarecurve( .data, .rare, .alpha = c("Observe", "Chao1", "ACE"), .group = NULL, nrow = 1, plot.group = FALSE, ... ) ## S4 method for signature 'tbl_mpse' mp_plot_rarecurve( .data, .rare, .alpha = c("Observe", "Chao1", "ACE"), .group = NULL, nrow = 1, plot.group = FALSE, ... ) ## S4 method for signature 'grouped_df_mpse' mp_plot_rarecurve( .data, .rare, .alpha = c("Observe", "Chao1", "ACE"), .group = NULL, nrow = 1, plot.group = FALSE, ... )
.data |
MPSE object or tbl_mpse after it was performed |
.rare |
the column names of |
.alpha |
the names of alpha index, which should be one or more of Observe, ACE, Chao1, default is Observe. |
.group |
the column names of group, default is NULL, when it is provided, the
rarecurve lines will group and color with the |
nrow |
integer Number of rows in |
plot.group |
logical whether to combine the samples, default is FALSE, when it is TRUE, the samples of same group will be represented by their group. |
... |
additional parameters, see also |
Shuangbin Xu
## Not run: data(mouse.time.mpse) mpse <- mouse.time.mpse %>% mp_rrarefy() mpse 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="Observe", .group=time) p3 <- mpse %>% mp_plot_rarecurve(.rare=RareAbundanceRarecurve, .alpha="Observe", .group=time, plot.group=TRUE) ## End(Not run)