mp_plot_ord {MicrobiotaProcess} | R Documentation

## Plotting the result of PCA, PCoA, CCA, RDA, NDMS or DCA

### Description

Plotting the result of PCA, PCoA, CCA, RDA, NDMS or DCA

### Usage

    mp_plot_ord(
      .data,
      .ord,
      .dim = c(1, 2),
      .group = NULL,
      .starshape = 15,
      .size = 2,
      .alpha = 1,
      .color = "black",
      starstroke = 0.5,
      show.side = TRUE,
      ellipse = FALSE,
      show.sample = FALSE,
      show.envfit = FALSE,
      p.adjust = NULL,
      filter.envfit = FALSE,
      ...
    )

    ## S4 method for signature 'MPSE'
    mp_plot_ord(
      .data,
      .ord,
      .dim = c(1, 2),
      .group = NULL,
      .starshape = 15,
      .size = 2,
      .alpha = 1,
      .color = "black",
      starstroke = 0.5,
      show.side = TRUE,
      ellipse = FALSE,
      show.sample = FALSE,
      show.envfit = FALSE,
      p.adjust = NULL,
      filter.envfit = FALSE,
      ...
    )

    ## S4 method for signature 'tbl_mpse'
    mp_plot_ord(
      .data,
      .ord,
      .dim = c(1, 2),
      .group = NULL,
      .starshape = 15,
      .size = 2,
      .alpha = 1,
      .color = "black",
      starstroke = 0.5,
      show.side = TRUE,
      ellipse = FALSE,
      show.sample = FALSE,
      show.envfit = FALSE,
      p.adjust = NULL,
      filter.envfit = FALSE,
      ...
    )

    ## S4 method for signature 'grouped_df_mpse'
    mp_plot_ord(
      .data,
      .ord,
      .dim = c(1, 2),
      .group = NULL,
      .starshape = 15,
      .size = 2,
      .alpha = 1,
      .color = "black",
      starstroke = 0.5,
      show.side = TRUE,
      ellipse = FALSE,
      show.sample = FALSE,
      show.envfit = FALSE,
      p.adjust = NULL,
      filter.envfit = FALSE,
      ...
    )

### Arguments

`.data` | MPSE or tbl_mpse object, it is required.
`.ord` | a name of ordination (required), options are PCA, PCoA, DCA, NMDS, RDA, CCA, but the corresponding calculation methods (mp_cal_pca, mp_cal_pcoa, ...) should be done with action="add" before it.
`.dim` | integer which dimensions will be displayed, it should be a vector (length=2) default is c(1, 2). if the length is one the default will also be displayed.
`.group` | the column name of variable to be mapped to the color of points (fill character of `geom_star`) or one specified color code, default is NULL, meaning `fill`=NA, the points are hollow.
`.starshape` | the column name of variable to be mapped to the shapes of points (starshape character of `geom_star`) or one specified `starshape` of point of `ggstar`, default is NULL, meaning `starshape`=15 (circle point).
`.size` | the column name of variable to be mapped to the size of points (size character of `geom_star`) or one specified `size` of point of `ggstar`, default is NULL, meaning the `size`=1.5, the size of points.
`.alpha` | the column name of variable to be mapped to the transparency of points (alpha character of `geom_star`) or one specified `alpha` of point of `ggstar`. default is NULL, meaning the `alpha`=1, the transparency of points.
`.color` | the column name of variable to be mapped to the color of line of points (color character of `geom_star`) or one specified `starshape` of point of `ggstar`, default is NULL, meaning the `color` is 'black'.
`starstroke` | numeric the width of edge of points, default is 0.5.
`show.side` | logical whether display the side boxplot with the specified `.dim` dimensions, default is TRUE.
`ellipse` | logical, whether to plot ellipses, default is FALSE. (.group or .color variables according to the 'geom', the default geom is path, so .color can be mapped to the corresponding variable).
`show.sample` | logical, whether display the sample names of points, default is FALSE.
`show.envfit` | logical, whether display the result after run [mp_envfit()], default is FALSE.
`p.adjust` | a character method of p.adjust `p.adjust`, default is NULL, options are 'fdr', 'bonferroni', 'BH' etc.
`filter.envfit` | logical or numeric, whether to remove the no significant environment factor after run [mp_envfit()], default is FALSE, meaning do not remove. If it is numeric, meaning the keep p.value or the adjust p with `p.adjust` the factors smaller than the numeric, e.g when filter.envfit=0.05 or (filter.envfit=TRUE), meaning the factors of p <= 0.05 will be displayed.
`...` | additional parameters, see also the `stat_ellipse`.

### See Also

[mp_cal_pca()], [mp_cal_pcoa], [mp_cal_nmds], [mp_cal_rda], [mp_cal_cca], [mp_envfit()] and [mp_extract_internal_attr()]

### Examples

    ## Not run:
    library(vegan)
    data(varespec, varechem)
    mpse <- MPSE(assays=list(Abundance=t(varespec)), colData=varechem)
    envformula <- paste("~", paste(colnames(varechem), collapse="+")) %>% as.formula
    mpse %<>%
    mp_cal_cca(.abundance=Abundance, .formula=envformula, action="add") %>%
    mp_envfit(.ord=CCA, .env=colnames(varechem), permutations=9999, action="add")
    mpse
    p1 <- mpse %>% mp_plot_ord(.ord=CCA, .group=Al, .size=Mn)
    p1
    p2 <- mpse %>% mp_plot_ord(.ord=CCA, .group=Al, .size=Mn, show.sample=TRUE)
    p2
    p3 <- mpse %>% mp_plot_ord(.ord=CCA, .group="blue", .size=Mn, .alpha=0.8, show.sample=TRUE)
    p3
    p4 <- mpse %>% mp_plot_ord(.ord=CCA, .group=Al, .size=Mn, show.sample=TRUE, show.envfit=TRUE)
    p4

    ## End(Not run)

[Package MicrobiotaProcess version 1.4.4 Index]