mp_plot_dist {MicrobiotaProcess} | R Documentation

## Plotting the distance between the samples with heatmap or boxplot.

### Description

Plotting the distance between the samples with heatmap or boxplot.

### Usage

    mp_plot_dist(
      .data,
      .distmethod,
      .group = NULL,
      group.test = FALSE,
      hclustmethod = "average",
      test = "wilcox.test",
      comparisons = NULL,
      step_increase = 0.1,
      ...
    )

    ## S4 method for signature 'MPSE'
    mp_plot_dist(
      .data,
      .distmethod,
      .group = NULL,
      group.test = FALSE,
      hclustmethod = "average",
      test = "wilcox.test",
      comparisons = NULL,
      step_increase = 0.1,
      ...
    )

    ## S4 method for signature 'tbl_mpse'
    mp_plot_dist(
      .data,
      .distmethod,
      .group = NULL,
      group.test = FALSE,
      hclustmethod = "average",
      test = "wilcox.test",
      comparisons = NULL,
      step_increase = 0.1,
      ...
    )

    ## S4 method for signature 'grouped_df_mpse'
    mp_plot_dist(
      .data,
      .distmethod,
      .group = NULL,
      group.test = FALSE,
      hclustmethod = "average",
      test = "wilcox.test",
      comparisons = NULL,
      step_increase = 0.1,
      ...
    )

### Arguments

`.data` | the MPSE or tbl_mpse object after [mp_cal_dist()] is performed with action="add"
`.distmethod` | the column names of distance of samples, it will generate after [mp_cal_dist()] is performed.
`.group` | the column names of group, default is NULL, when it is not provided the heatmap of distance between samples will be returned. If it is provided and `group.test` is TURE, the comparisons boxplot of distance between the group will be returned, but when `group.test` is FALSE, the heatmap of distance between samples with group information will be returned.
`group.test` | logical default is FALSE, see the `.group` argument.
`hclustmethod` | character the method of `hclust`, default is 'average' (= UPGMA).
`test` | the name of the statistical test, default is 'wilcox.test'
`comparisons` | A list of length-2 vectors. The entries in the vector are either the names of 2 values on the x-axis or the 2 integers that correspond to the index of the columns of interest, default is NULL, meaning it will be calculated automatically with the names in the .group.
`step_increase` | numeric vector with the increase in fraction of total height for every additional comparison to minimize overlap, default is 0.1.
`...` | additional parameters, see also `geom_signif`

### Author(s)

Shuangbin Xu

### See Also

[mp_cal_dist()] and [mp_extract_dist()]

### Examples

    ## Not run:
    data(mouse.time.mpse)
    mouse.time.mpse %<>% mp_decostand(.abundance=Abundance)
    mouse.time.mpse
    mouse.time.mpse %<>%
      mp_cal_dist(.abundance=hellinger, distmethod="bray")
    mouse.time.mpse
    p1 <- mouse.time.mpse %>%
            mp_plot_dist(.distmethod=bray)
    p2 <- mouse.time.mpse %>%
            mp_plot_dist(.distmethod=bray, .group=time, group.test=TRUE)
    p3 <- mouse.time.mpse %>%
            mp_plot_dist(.distmethod=bray, .group=time)

    ## End(Not run)

[Package MicrobiotaProcess version 1.4.4 Index]