trans_abund: Create trans_abund object to transform taxonomic abundance...

Description Methods Examples

Description

This class is a wrapper for the taxonomic abundance transformations and plotting. The transformed data style is the long-format for ggplot2 plotting. The plotting approaches include the bar plot, boxplot, heatmap and pie chart based on An et al. (2019) <doi:10.1016/j.geoderma.2018.09.035>.

Methods

Public methods


Method new()

Usage
trans_abund$new(
  dataset = NULL,
  taxrank = "Phylum",
  show = 0,
  ntaxa = 10,
  groupmean = NULL,
  delete_full_prefix = TRUE,
  delete_part_prefix = FALSE,
  prefix = NULL,
  use_percentage = TRUE,
  input_taxaname = NULL
)
Arguments
dataset

The microtable class.

taxrank

default "Phylum"; taxonomic rank.

show

default 0; the relative abundance threshold.

ntaxa

default 10; how many taxa will be used, ordered by abundance from high to low.

groupmean

default NULL; for calculating mean abundance, select a group column name in sample_table.

delete_full_prefix

default TRUE; whether delete the prefix and the character in front of them.

delete_part_prefix

default TRUE; whether only delete the prefix.

prefix

default NULL; character string; used when delete_full_prefix = T or delete_part_prefix = T; default reprensents using the "letter+__", e.g. "k__" for Phylum level.

use_percentage

default TRUE; showing the abundance percentage.

input_taxaname

default NULL; if some taxa are selected, input taxa names.

Returns

abund_data and other file for plotting.

Examples
\donttest{
data(dataset)
t1 <- trans_abund$new(dataset = dataset, taxrank = "Phylum", ntaxa = 10)
}

Method plot_bar()

Plot the bar plot with the object of trans_abund Class.

Usage
trans_abund$plot_bar(
  use_colors = RColorBrewer::brewer.pal(12, "Paired"),
  bar_type = "full",
  others_color = "grey90",
  facet = NULL,
  order_facet = NULL,
  x_axis_name = NULL,
  order_x = NULL,
  barwidth = NULL,
  use_alluvium = FALSE,
  clustering = FALSE,
  facet_color = "grey95",
  strip_text = 11,
  legend_text_italic = FALSE,
  xtext_type_hor = TRUE,
  xtext_size = 10,
  xtext_keep = TRUE,
  xtitle_keep = TRUE,
  ytitle_size = 17,
  base_font = NULL,
  ylab_title = NULL
)
Arguments
use_colors

default RColorBrewer::brewer.pal(12, "Paired"); providing the plotting colors.

bar_type

default "full"; "full" or "notfull"; if full, the total abundance sum to 1 or 100 percentage.

others_color

default "grey90"; the color for "others" taxa.

facet

default NULL; a character string; if using facet, providing a group column name of sample_table, such as, "Group".

order_facet

NULL; vector; used to order the facet, such as, c("Group1", "Group3", "Group2").

x_axis_name

NULL; a character string; a column name of sample_table used to show the sample names in x axis.

order_x

default NULL; vector; used to order the sample names in x axis; must be the samples vector, such as, c("S1", "S3", "S2").

barwidth

default NULL; bar width, see width in geom_bar.

use_alluvium

default FALSE; whether add alluvium plot

clustering

default FALSE; whether order samples by the clustering

facet_color

default "grey95"; facet background color.

strip_text

default 11; facet text size.

legend_text_italic

default FALSE; whether use italic in legend.

xtext_type_hor

default TRUE; x axis text horizontal, if FALSE; text slant.

xtext_size

default 10; x axis text size.

xtext_keep

default TRUE; whether retain x text.

xtitle_keep

default TRUE; whether retain x title.

ytitle_size

default 17; y axis title size.

base_font

default NULL; ggplot font family in the plot.

ylab_title

default NULL; y axis title.

Returns

ggplot2 plot.

Examples
\donttest{
t1$plot_bar(facet = "Group", xtext_keep = FALSE)
}

Method plot_heatmap()

Plot the heatmap with the object of trans_abund Class.

Usage
trans_abund$plot_heatmap(
  use_colors = c("#00008B", "#102D9B", "#215AAC", "#3288BD", "#66C2A5", "#E6F598",
    "#FFFFBF", "#FED690", "#FDAE61", "#F46D43", "#D53E4F", "#9E0142"),
  facet = NULL,
  order_facet = NULL,
  x_axis_name = NULL,
  order_x = NULL,
  withmargin = TRUE,
  plot_numbers = FALSE,
  plot_text_size = 4,
  plot_breaks = NULL,
  margincolor = "white",
  plot_colorscale = "log10",
  min_abundance = 0.01,
  max_abundance = NULL,
  strip_text = 11,
  xtext_size = 10,
  ytext_size = 11,
  xtext_keep = TRUE,
  xtitle_keep = TRUE,
  grid_clean = TRUE,
  xtext_type_hor = TRUE,
  base_font = NULL
)
Arguments
use_colors

default RColorBrewer::brewer.pal(12, "Paired"); providing the plotting colors.

facet

default NULL; a character string; if using facet, providing a group column name of sample_table, such as, "Group".

order_facet

NULL; vector; used to order the facet, such as, c("Group1", "Group3", "Group2").

x_axis_name

NULL; a character string; a column name of sample_table used to show the sample names in x axis.

order_x

default NULL; vector; used to order the sample names in x axis; must be the samples vector, such as, c("S1", "S3", "S2").

withmargin

default TRUE; whether retain the tile margin.

plot_numbers

default FALSE; whether plot the number in heatmap.

plot_text_size

default 4; If plot_numbers TRUE, text size in plot.

plot_breaks

default NULL; The legend breaks.

margincolor

default "white"; If withmargin TRUE, use this as the margin color.

plot_colorscale

default "log10"; color scale.

min_abundance

default .01; the minimum abundance percentage in plot.

max_abundance

default NULL; the maximum abundance percentage in plot, NULL reprensent the max percentage.

strip_text

default 11; facet text size.

xtext_size

default 10; x axis text size.

ytext_size

default 11; y axis text size.

xtext_keep

default TRUE; whether retain x text.

xtitle_keep

default TRUE; whether retain x title.

grid_clean

default TRUE; whether remove grid lines.

xtext_type_hor

default TRUE; x axis text horizontal, if FALSE; text slant.

base_font

default NULL; font in the plot.

Returns

ggplot2 plot.

Examples
\donttest{
t1 <- trans_abund$new(dataset = dataset, taxrank = "Genus", ntaxa = 40)
t1$plot_heatmap(facet = "Group", xtext_keep = FALSE, withmargin = FALSE)
}

Method plot_box()

Plot the box plot with the object of trans_abund Class.

Usage
trans_abund$plot_box(
  use_colors = RColorBrewer::brewer.pal(8, "Dark2"),
  group = NULL,
  show_point = FALSE,
  point_color = "black",
  point_size = 3,
  point_alpha = 0.3,
  plot_flip = FALSE,
  boxfill = TRUE,
  middlecolor = "grey95",
  middlesize = 1,
  xtext_type_hor = FALSE,
  xtext_size = 10,
  xtext_keep = TRUE,
  xtitle_keep = TRUE,
  ytitle_size = 17,
  base_font = NULL,
  ...
)
Arguments
use_colors

default RColorBrewer::brewer.pal(12, "Paired"); providing the plotting colors.

group

default NULL; column name of sample table to show abundance across groups.

show_point

default FALSE; whether show points in plot.

point_color

default "black"; If show_point TRUE; use the color

point_size

default 3; If show_point TRUE; use the size

point_alpha

default .3; If show_point TRUE; use the transparency.

plot_flip

default FALSE; Whether rotate plot.

boxfill

default TRUE; Whether fill the box.

middlecolor

default "grey95"; The middle line color.

middlesize

default 1; The middle line size.

xtext_type_hor

default TRUE; x axis text horizontal, if FALSE; text slant.

xtext_size

default 10; x axis text size.

xtext_keep

default TRUE; whether retain x text.

xtitle_keep

default TRUE; whether retain x title.

ytitle_size

default 17; y axis title size.

base_font

default NULL; font in the plot.

...

parameters pass to geom_boxplot.

Returns

ggplot2 plot.

Examples
\donttest{
t1$plot_box(group = "Group")
}

Method plot_pie()

Plot pie chart with the object of trans_abund Class.

Usage
trans_abund$plot_pie(
  use_colors = RColorBrewer::brewer.pal(8, "Dark2"),
  facet_nrow = 1,
  strip_text = 11,
  legend_text_italic = FALSE
)
Arguments
use_colors

default RColorBrewer::brewer.pal(8, "Dark2"); providing the plotting colors.

facet_nrow

default 1; how many rows in the plot.

strip_text

default 11; sample title size.

legend_text_italic

default FALSE; whether use italic in legend.

Returns

ggplot2 plot.

Examples
\donttest{
t1 <- trans_abund$new(dataset = dataset, taxrank = "Phylum", ntaxa = 6, groupmean = "Group")
t1$plot_pie(facet_nrow = 1)
}

Method print()

Print the trans_abund object.

Usage
trans_abund$print()

Method clone()

The objects of this class are cloneable with this method.

Usage
trans_abund$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

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## ------------------------------------------------
## Method `trans_abund$new`
## ------------------------------------------------


data(dataset)
t1 <- trans_abund$new(dataset = dataset, taxrank = "Phylum", ntaxa = 10)


## ------------------------------------------------
## Method `trans_abund$plot_bar`
## ------------------------------------------------


t1$plot_bar(facet = "Group", xtext_keep = FALSE)


## ------------------------------------------------
## Method `trans_abund$plot_heatmap`
## ------------------------------------------------


t1 <- trans_abund$new(dataset = dataset, taxrank = "Genus", ntaxa = 40)
t1$plot_heatmap(facet = "Group", xtext_keep = FALSE, withmargin = FALSE)


## ------------------------------------------------
## Method `trans_abund$plot_box`
## ------------------------------------------------


t1$plot_box(group = "Group")


## ------------------------------------------------
## Method `trans_abund$plot_pie`
## ------------------------------------------------


t1 <- trans_abund$new(dataset = dataset, taxrank = "Phylum", ntaxa = 6, groupmean = "Group")
t1$plot_pie(facet_nrow = 1)

microeco documentation built on May 30, 2021, 5:06 p.m.