mp_cal_alpha {MicrobiotaProcess} | R Documentation

## 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, J))
    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)

[Package MicrobiotaProcess version 1.4.4 Index]