mp_plot_diff_boxplot-methods: displaying the differential result contained abundance and...

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

displaying the differential result contained abundance and LDA with boxplot (abundance) and error bar (LDA).

Description

displaying the differential result contained abundance and LDA with boxplot (abundance) and error bar (LDA).

Usage

mp_plot_diff_boxplot(
  .data,
  .group,
  .size = 2,
  errorbar.xmin = NULL,
  errorbar.xmax = NULL,
  point.x = NULL,
  taxa.class = "all",
  group.abun = FALSE,
  removeUnknown = FALSE,
  ...
)

## S4 method for signature 'MPSE'
mp_plot_diff_boxplot(
  .data,
  .group,
  .size = 2,
  errorbar.xmin = NULL,
  errorbar.xmax = NULL,
  point.x = NULL,
  taxa.class = "all",
  group.abun = FALSE,
  removeUnknown = FALSE,
  ...
)

## S4 method for signature 'tbl_mpse'
mp_plot_diff_boxplot(
  .data,
  .group,
  .size = 2,
  errorbar.xmin = NULL,
  errorbar.xmax = NULL,
  point.x = NULL,
  taxa.class = "all",
  group.abun = FALSE,
  removeUnknown = FALSE,
  ...
)

## S4 method for signature 'grouped_df_mpse'
mp_plot_diff_boxplot(
  .data,
  .group,
  .size = 2,
  errorbar.xmin = NULL,
  errorbar.xmax = NULL,
  point.x = NULL,
  taxa.class = "all",
  group.abun = FALSE,
  removeUnknown = FALSE,
  ...
)

Arguments

.data	MPSE or tbl_mpse after run mp_diff_analysis with 'action="add"'.
.group	the column name for mapping the different color.
.size	the column name for mapping the size of points or numeric, default is 2.
errorbar.xmin	the column name for 'xmin' mapping of error barplot layer, default is NULL.
errorbar.xmax	the column name for 'xmax' mapping of error barplot layer, default is NULL.
point.x	the column name for 'x' mapping of point layer (right panel), default is NULL.
taxa.class	the taxonomy class features will be displayed, default is 'all'.
group.abun	logical whether plot the abundance in each group with bar plot, default is FALSE.
removeUnknown	logical whether mask the unknown taxonomy information but differential species, default is FALSE.
...	additional params, see also the 'geom_boxplot', 'geom_errorbarh' and 'geom_point'.

Examples

data(mouse.time.mpse)
mouse.time.mpse %<>%
  mp_rrarefy()
mouse.time.mpse
mouse.time.mpse %<>%
  mp_diff_analysis(.abundance=RareAbundance,
                   .group=time,
                   first.test.alpha=0.01,
                   action="add")
library(ggplot2)
p1 <- mouse.time.mpse %>% 
        mp_plot_diff_boxplot(.group = time) %>%
        set_diff_boxplot_color(
          values = c("deepskyblue", "orange"),
          guide = guide_legend(title=NULL)
        )
p1
p2 <- mouse.time.mpse %>% 
        mp_plot_diff_boxplot(
          taxa.class = c(Genus, OTU),
          group.abun = TRUE, 
          removeUnknown = TRUE,
        ) %>%
        set_diff_boxplot_color(
          values = c("deepskyblue", "orange"),
          guide = guide_legend(title=NULL)
        )
p2 

xiangpin/MicrobiotaProcess documentation built on Nov. 12, 2024, 2:05 p.m.