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

mp_plot_diff_manhattanR Documentation

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.