mp_cal_alpha-methods: calculate the alpha index with MPSE or tbl_mpse

In YuLab-SMU/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

calculate the alpha index with MPSE or tbl_mpse

Description

calculate the alpha index with MPSE or tbl_mpse

Usage

mp_cal_alpha(
  .data,
  .abundance = NULL,
  action = c("add", "only", "get"),
  force = FALSE,
  ...
)

## S4 method for signature 'MPSE'
mp_cal_alpha(.data, .abundance = NULL, action = "add", force = FALSE, ...)

## S4 method for signature 'tbl_mpse'
mp_cal_alpha(.data, .abundance = NULL, action = "add", force = FALSE, ...)

## S4 method for signature 'grouped_df_mpse'
mp_cal_alpha(.data, .abundance = NULL, action = "add", force = FALSE, ...)

Arguments

.data	MPSE or tbl_mpse object
.abundance	The column name of OTU abundance column to be calculate
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 'alphasample' object.
force	logical whether calculate the alpha index even the '.abundance' is not rarefied, default is FALSE.
...	additional arguments

Value

update object or other (refer to action)

Author(s)

Shuangbin Xu

See Also

[mp_plot_alpha()]

Examples

data(mouse.time.mpse)
mpse <- mouse.time.mpse %>% 
        mp_rrarefy() %>%
        mp_cal_alpha(.abundance=RareAbundance)
mpse
p <- mpse %>% mp_plot_alpha(.group=time, .alpha=c(Observe, Shannon, Pielou))
p
# Or you can extract the result and visualize it with ggplot2 and ggplot2-extensions
## Not run: 
tbl <- mpse %>% 
       mp_extract_sample
tbl
tbl %<>% 
  tidyr::pivot_longer(cols=!c("Sample", "time"), names_to="measure", values_to="alpha")
tbl
library(ggplot2)
library(ggsignif)
library(gghalves)
p <- ggplot(data=tbl, aes(x=time, y=alpha, fill=time)) + 
     geom_half_violin(color=NA, side="l", trim=FALSE) + 
     geom_boxplot(aes(color=time), fill=NA, position=position_nudge(x=.22), width=0.2) + 
     geom_half_point(side="r", shape=21) + 
     geom_signif(comparisons=list(c("Early", "Late")), test="wilcox.test", textsize=2) + 
     facet_wrap(facet=vars(measure), scales="free_y", nrow=1) +
     scale_fill_manual(values=c("#00A087FF", "#3C5488FF")) + 
     scale_color_manual(values=c("#00A087FF", "#3C5488FF"))
p

## End(Not run)

YuLab-SMU/MicrobiotaProcess documentation built on July 26, 2024, 4:21 a.m.