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

In YuLab-SMU/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 manhattan plot.

Description

displaying the differential result contained abundance and LDA with manhattan plot.

Usage

mp_plot_diff_manhattan(
  .data,
  .group,
  .y = "fdr",
  .size = 2,
  taxa.class = "OTU",
  anno.taxa.class = NULL,
  removeUnknown = FALSE,
  ...
)

## S4 method for signature 'MPSE'
mp_plot_diff_manhattan(
  .data,
  .group,
  .y = "fdr",
  .size = 2,
  taxa.class = "OTU",
  anno.taxa.class = NULL,
  removeUnknown = FALSE,
  ...
)

## S4 method for signature 'tbl_mpse'
mp_plot_diff_manhattan(
  .data,
  .group,
  .y = "fdr",
  .size = 2,
  taxa.class = "OTU",
  anno.taxa.class = NULL,
  removeUnknown = FALSE,
  ...
)

## S4 method for signature 'grouped_df_mpse'
mp_plot_diff_manhattan(
  .data,
  .group,
  .y = "fdr",
  .size = 2,
  taxa.class = "OTU",
  anno.taxa.class = NULL,
  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.
.y	the column name for mapping the y axis, default is 'fdr'.
.size	the column name for mapping the size of points or numeric, default is 2.
taxa.class	the taxonomy class features will be displayed, default is 'OTU'.
anno.taxa.class	the taxonomy class to annotate the sign taxa with color, default is 'Phylum' if 'taxatree' is not empty.
removeUnknown	logical whether mask the unknown taxonomy information but differential species, default is FALSE.
...	additional params, see also the 'geom_text_repel' 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")
p <- mouse.time.mpse %>% 
       mp_plot_diff_manhattan(
           .group = Sign_time, 
           .y = fdr,
           .size = 2,
           taxa.class = OTU,
           anno.taxa.class = Phylum,
       )

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