R: Create 'trans_abund' object for taxonomic abundance...

trans_abund {microeco}

R Documentation

Create `trans_abund` object for taxonomic abundance visualization.

Description

This class is a wrapper for the taxonomic abundance transformations and visualization. The converted data style is the long-format for ggplot2 plot. The plotting methods include bar plot, boxplot, heatmap, pie chart and line chart.

Methods

Method `new()`

Usage

trans_abund$new(
  dataset = NULL,
  taxrank = "Phylum",
  show = 0,
  ntaxa = 10,
  groupmean = NULL,
  group_morestats = FALSE,
  delete_taxonomy_lineage = TRUE,
  delete_taxonomy_prefix = TRUE,
  prefix = NULL,
  use_percentage = TRUE,
  input_taxaname = NULL,
  high_level = NULL,
  high_level_fix_nsub = NULL
)

Arguments

dataset: default NULL; the object of microtable class.
taxrank: default "Phylum"; taxonomic rank.
show: default 0; the relative abundance threshold for filtering the taxa with low abundance.
ntaxa: default 10; how many taxa are selected to show. Taxa are ordered by abundance from high to low. This parameter does not conflict with the parameter show. Both can be used. ntaxa = NULL means it is unavailable.
groupmean: default NULL; calculate mean abundance for each group. Select a column name in microtable$sample_table.
group_morestats: default FALSE; only available when groupmean parameter is provided; Whether output more statistics for each group, including min, max, median and quantile; Thereinto, quantile25 and quantile75 denote 25% and 75% quantiles, respectively.
delete_taxonomy_lineage: default TRUE; whether delete the taxonomy lineage in front of the target level.
delete_taxonomy_prefix: default TRUE; whether delete the prefix of taxonomy, such as "g__".
prefix: default NULL; character string; available when delete_taxonomy_prefix = T; default NULL represents using the "letter+__", e.g. "k__" for Phylum level; Please provide the customized prefix when it is not standard, otherwise the program can not correctly recognize it.
use_percentage: default TRUE; show the abundance percentage.
input_taxaname: default NULL; character vector; input taxa names to select some taxa.
high_level: default NULL; a taxonomic rank, such as "Phylum", used to add the taxonomic information of higher level. It is necessary for the legend with nested taxonomic levels in the bar plot.
high_level_fix_nsub: default NULL; an integer, used to fix the number of selected abundant taxa in each taxon from higher taxonomic level. If the total number under one taxon of higher level is less than the high_level_fix_nsub, the total number will be used. When high_level_fix_nsub is provided, the taxa number of higher level is calculated as: ceiling(ntaxa/high_level_fix_nsub). Note that ntaxa means either the parameter ntaxa or the taxonomic number obtained by filtering according to the show parameter.

Returns

data_abund stored in the object. The column 'all_mean_abund' represents mean relative abundance across all the samples. So the values in one taxon are all same across all the samples. If the sum of column 'Abundance' in one sample is larger than 1, the 'Abundance', 'SD' and 'SE' has been multiplied by 100.

Examples

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

Method `plot_bar()`

Bar plot.

Usage

trans_abund$plot_bar(
  color_values = RColorBrewer::brewer.pal(8, "Dark2"),
  bar_full = TRUE,
  others_color = "grey90",
  facet = NULL,
  order_x = NULL,
  x_axis_name = NULL,
  barwidth = NULL,
  use_alluvium = FALSE,
  clustering = FALSE,
  clustering_plot = FALSE,
  cluster_plot_width = 0.2,
  facet_color = "grey95",
  strip_text = 11,
  legend_text_italic = FALSE,
  xtext_angle = 0,
  xtext_size = 10,
  xtext_keep = TRUE,
  xtitle_keep = TRUE,
  ytitle_size = 17,
  coord_flip = FALSE,
  ggnested = FALSE,
  high_level_add_other = FALSE,
  ...
)

Arguments

color_values: default RColorBrewer::brewer.pal(8, "Dark2"); colors palette for the bars.
bar_full: default TRUE; Whether the bar shows all the features (including 'Others'). Default TRUE means total abundance are summed to 1 or 100 (percentage). FALSE means 'Others' will not be shown.
others_color: default "grey90"; the color for "Others" taxa.
facet: default NULL; a character vector for the facet; group column name of sample_table, such as, "Group"; If multiple facets are needed, please provide ordered names, such as c("Group", "Type"). The latter should have a finer scale than the former one; Please adjust the facet orders in the plot by assigning factors in sample_table before creating trans_abund object or assigning factors in the data_abund table of trans_abund object. When multiple facets are used, please first install package ggh4x using the command install.packages("ggh4x").
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").
x_axis_name: NULL; a character string; a column name of sample_table in dataset; used to show the sample names in x axis.
barwidth: default NULL; bar width, see width in geom_bar.
use_alluvium: default FALSE; whether add alluvium plot. If TRUE, please first install ggalluvial package.
clustering: default FALSE; whether order samples by the clustering.
clustering_plot: default FALSE; whether add clustering plot. If clustering_plot = TRUE, clustering will be also TRUE in any case for the clustering.
cluster_plot_width: default 0.2, the dendrogram plot width; available when clustering_plot = TRUE.
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_angle: default 0; number ranging from 0 to 90; used to adjust x axis text angle to reduce text overlap;
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.
coord_flip: default FALSE; whether flip cartesian coordinates so that horizontal becomes vertical, and vertical becomes horizontal.
ggnested: default FALSE; whether use nested legend. Need ggnested package to be installed (https://github.com/gmteunisse/ggnested). To make it available, please assign high_level parameter when creating the object.
high_level_add_other: default FALSE; whether add 'Others' (all the unknown taxa) in each taxon of higher taxonomic level. Only available when ggnested = TRUE.
...: Capture unknown parameters.

Returns

ggplot2 object.

Examples

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

Method `plot_heatmap()`

Plot the heatmap.

Usage

trans_abund$plot_heatmap(
  color_values = rev(RColorBrewer::brewer.pal(n = 11, name = "RdYlBu")),
  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_angle = 0,
  legend_title = "% Relative\nAbundance",
  pheatmap = FALSE,
  ...
)

Arguments

color_values: default rev(RColorBrewer::brewer.pal(n = 11, name = "RdYlBu")); colors palette for the plotting.
facet: default NULL; a character vector for the facet; a group column name of sample_table, such as, "Group"; If multiple facets are needed, please provide ordered names, such as c("Group", "Type"). The latter should have a finer scale than the former one; Please adjust the facet orders in the plot by assigning factors in sample_table before creating trans_abund object or assigning factors in the data_abund table of trans_abund object. When multiple facets are used, please first install package ggh4x using the command install.packages("ggh4x").
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_angle: default 0; number ranging from 0 to 90; used to adjust x axis text angle to reduce text overlap;
legend_title: default "% Relative\nAbundance"; legend title text.
pheatmap: default FALSE; whether use pheatmap package to plot the heatmap.
...: paremeters pass to pheatmap when pheatmap = TRUE.

Returns

ggplot2 object or grid object based on pheatmap.

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()`

Box plot.

Usage

trans_abund$plot_box(
  color_values = 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_angle = 0,
  xtext_size = 10,
  ytitle_size = 17,
  ...
)

Arguments

color_values: default RColorBrewer::brewer.pal(8, "Dark2"); colors palette for the box.
group: default NULL; a 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 with colors.
middlecolor: default "grey95"; The middle line color.
middlesize: default 1; The middle line size.
xtext_angle: default 0; number ranging from 0 to 90; used to adjust x axis text angle to reduce text overlap;
xtext_size: default 10; x axis text size.
ytitle_size: default 17; y axis title size.
...: parameters pass to geom_boxplot function.

Returns

ggplot2 object.

Examples

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

Method `plot_line()`

Plot the line chart.

Usage

trans_abund$plot_line(
  color_values = RColorBrewer::brewer.pal(8, "Dark2"),
  plot_SE = TRUE,
  position = position_dodge(0.1),
  errorbar_size = 1,
  errorbar_width = 0.1,
  point_size = 3,
  point_alpha = 0.8,
  line_size = 0.8,
  line_alpha = 0.8,
  line_type = 1,
  xtext_angle = 0,
  xtext_size = 10,
  ytitle_size = 17
)

Arguments

color_values: default RColorBrewer::brewer.pal(8, "Dark2"); colors palette for the points and lines.
plot_SE: default TRUE; TRUE: the errorbar is mean±se; FALSE: the errorbar is mean±sd.
position: default position_dodge(0.1); Position adjustment, either as a string (such as "identity"), or the result of a call to a position adjustment function.
errorbar_size: default 1; errorbar line size.
errorbar_width: default 0.1; errorbar width.
point_size: default 3; point size for taxa.
point_alpha: default 0.8; point transparency.
line_size: default 0.8; line size.
line_alpha: default 0.8; line transparency.
line_type: default 1; an integer; line type.
xtext_angle: default 0; number ranging from 0 to 90; used to adjust x axis text angle to reduce text overlap;
xtext_size: default 10; x axis text size.
ytitle_size: default 17; y axis title size.

Returns

ggplot2 object.

Examples

\donttest{
t1 <- trans_abund$new(dataset = dataset, taxrank = "Genus", ntaxa = 5)
t1$plot_line(point_size = 3)
t1 <- trans_abund$new(dataset = dataset, taxrank = "Genus", ntaxa = 5, groupmean = "Group")
t1$plot_line(point_size = 5, errorbar_size = 1, xtext_angle = 30)
}

Method `plot_pie()`

Pie chart.

Usage

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

Arguments

color_values: default RColorBrewer::brewer.pal(8, "Dark2"); colors palette for each section.
facet_nrow: default 1; how many rows in the plot.
strip_text: default 11; sample title size.
add_label: default FALSE; Whether add the percentage label in each section of pie chart.
legend_text_italic: default FALSE; whether use italic in legend.

Returns

ggplot2 object.

Examples

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

Method `plot_donut()`

Donut chart based on the ggpubr::ggdonutchart function.

Usage

trans_abund$plot_donut(
  color_values = RColorBrewer::brewer.pal(8, "Dark2"),
  label = TRUE,
  facet_nrow = 1,
  legend_text_italic = FALSE,
  ...
)

Arguments

color_values: default RColorBrewer::brewer.pal(8, "Dark2"); colors palette for the donut.
label: default TRUE; whether show the percentage label.
facet_nrow: default 1; how many rows in the plot.
legend_text_italic: default FALSE; whether use italic in legend.
...: parameters passed to ggpubr::ggdonutchart.

Returns

combined ggplot2 objects list, generated by ggpubr::ggarrange function.

Examples

\dontrun{
t1 <- trans_abund$new(dataset = dataset, taxrank = "Phylum", ntaxa = 6, groupmean = "Group")
t1$plot_donut(label = TRUE)
}

Method `plot_radar()`

Radar chart based on the ggradar package (https://github.com/ricardo-bion/ggradar).

Usage

trans_abund$plot_radar(
  color_values = RColorBrewer::brewer.pal(8, "Dark2"),
  ...
)

Arguments

color_values: default RColorBrewer::brewer.pal(8, "Dark2"); colors palette for samples.
...: parameters passed to ggradar::ggradar function except group.colours parameter.

Returns

ggplot2 object.

Examples

\dontrun{
t1 <- trans_abund$new(dataset = dataset, taxrank = "Phylum", ntaxa = 6, groupmean = "Group")
t1$plot_radar()
}

Method `plot_tern()`

Ternary diagrams based on the ggtern package.

Usage

trans_abund$plot_tern(
  color_values = RColorBrewer::brewer.pal(8, "Dark2"),
  color_legend_guide_size = 4
)

Arguments

color_values: default RColorBrewer::brewer.pal(8, "Dark2"); colors palette for the samples.
color_legend_guide_size: default 4; The size of legend guide for color.

Returns

ggplot2 object.

Examples

\dontrun{
t1 <- trans_abund$new(dataset = dataset, taxrank = "Phylum", ntaxa = 6, groupmean = "Group")
t1$plot_tern()
}

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


## ------------------------------------------------
## 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_line`
## ------------------------------------------------


t1 <- trans_abund$new(dataset = dataset, taxrank = "Genus", ntaxa = 5)
t1$plot_line(point_size = 3)
t1 <- trans_abund$new(dataset = dataset, taxrank = "Genus", ntaxa = 5, groupmean = "Group")
t1$plot_line(point_size = 5, errorbar_size = 1, xtext_angle = 30)


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


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


## ------------------------------------------------
## Method `trans_abund$plot_donut`
## ------------------------------------------------

## Not run: 
t1 <- trans_abund$new(dataset = dataset, taxrank = "Phylum", ntaxa = 6, groupmean = "Group")
t1$plot_donut(label = TRUE)

## End(Not run)

## ------------------------------------------------
## Method `trans_abund$plot_radar`
## ------------------------------------------------

## Not run: 
t1 <- trans_abund$new(dataset = dataset, taxrank = "Phylum", ntaxa = 6, groupmean = "Group")
t1$plot_radar()

## End(Not run)

## ------------------------------------------------
## Method `trans_abund$plot_tern`
## ------------------------------------------------

## Not run: 
t1 <- trans_abund$new(dataset = dataset, taxrank = "Phylum", ntaxa = 6, groupmean = "Group")
t1$plot_tern()

## End(Not run)

[Package microeco version 1.8.0 Index]

Create trans_abund object for taxonomic abundance visualization.

Description

Methods

Public methods

Method new()

Usage

Arguments

Returns

Examples

Method plot_bar()

Usage

Arguments

Returns

Examples

Method plot_heatmap()

Usage

Arguments

Returns

Examples

Method plot_box()

Usage

Arguments

Returns

Examples

Method plot_line()

Usage

Arguments

Returns

Examples

Method plot_pie()

Usage

Arguments

Returns

Examples

Method plot_donut()

Usage

Arguments

Returns

Examples

Method plot_radar()

Usage

Arguments

Returns

Examples

Method plot_tern()

Usage

Arguments

Returns

Examples

Method print()

Usage

Method clone()

Usage

Arguments

Examples

Create `trans_abund` object for taxonomic abundance visualization.

Method `new()`

Method `plot_bar()`

Method `plot_heatmap()`

Method `plot_box()`

Method `plot_line()`

Method `plot_pie()`

Method `plot_donut()`

Method `plot_radar()`

Method `plot_tern()`

Method `print()`

Method `clone()`