plotAbundanceDensity: Plot abundance density

In microbiome/miaViz: Microbiome Analysis Plotting and Visualization

Plot abundance density

Description

This function plots abundance of the most abundant taxa.

Usage

plotAbundanceDensity(object, ...)

## S4 method for signature 'SummarizedExperiment'
plotAbundanceDensity(
  object,
  layout = c("jitter", "density", "point"),
  assay.type = assay_name,
  assay_name = "counts",
  n = min(nrow(object), 25L),
  colour_by = NULL,
  shape_by = NULL,
  size_by = NULL,
  order_descending = TRUE,
  ...
)

Arguments

object	a SummarizedExperiment object.
...	additional parameters for plotting. xlab a single character value for selecting the x-axis label. (default: xlab = assay.type) ylab a single character value for selecting the y-axis label. ylab is disabled when layout = "density". (default: ylab = "Taxa") point_alpha a numeric value from range 0 to 1 selecting the transparency of colour in jitter and point plot. (default: point_alpha = 0.6) point_shape a positive integer value selecting the shape of point in jitter and point plot. (default: point_shape = 21) point_size a positive numeric value selecting the size of point in jitter and point plot. (default: point_size = 2) add_legend a boolean value selecting if legend is added. (default: add_legend = TRUE) flipped a boolean value selecting if the orientation of plot is changed so that x-axis and y-axis are swapped. (default flipped = FALSE) add_x_text a boolean value selecting if text that represents values is included in x-axis. (default: add_x_text = TRUE) See mia-plot-args for more details i.e. call help("mia-plot-args")
layout	a single character value for selecting the layout of the plot. There are three different options: jitter, density, and point plot. (default: layout = "jitter")
assay.type	a single character value for selecting the assay to be plotted. (default: assay.type = "counts")
assay_name	a single character value for specifying which assay to use for calculation. (Please use assay.type instead. At some point assay_name will be disabled.)
n	a positive integer specifying the number of the most abundant taxa to show. (default: n = min(nrow(object), 25L))
colour_by	a single character value defining a column from colData, that is used to color plot. Must be a value of colData() function. (default: colour_by = NULL)
shape_by	a single character value defining a column from colData, that is used to group observations to different point shape groups. Must be a value of colData() function. shape_by is disabled when layout = "density". (default: shape_by = NULL)
size_by	a single character value defining a column from colData, that is used to group observations to different point size groups. Must be a value of colData() function. size_by is disabled when layout = "density". (default: size_by = NULL)
order_descending	TRUE, FALSE orNA: Should the results be ordered in a descending order? If NA is given the order as found in object for the n most abundant taxa is used. (default: order_descending = TRUE)

Details

This function plots abundance of the most abundant taxa. Abundance can be plotted as a jitter plot, a density plot, or a point plot. By default, x-axis represents abundance and y-axis taxa. In a jitter and point plot, each point represents abundance of individual taxa in individual sample. Most common abundances are shown as a higher density.

A density plot can be seen as a smoothened bar plot. It visualized distribution of abundances where peaks represent most common abundances.

Value

A ggplot2 object

Author(s)

Leo Lahti and Tuomas Borman. Contact: microbiome.github.io

Examples

tse <- microbiomeDataSets::atlas1006()

# Plots the abundances of 25 most abundant taxa. Jitter plot is the default option.
plotAbundanceDensity(tse, assay.type = "counts")

# Counts relative abundances
tse <- transformAssay(tse, method = "relabundance")

# Plots the relative abundance of 10 most abundant taxa. 
# "nationality" information is used to color the points. X-axis is log-scaled.
plotAbundanceDensity(tse, layout = "jitter", assay.type = "relabundance", 
                     n = 10, colour_by = "nationality") +
    scale_x_log10() 
                     
# Plots the relative abundance of 10 most abundant taxa as a density plot.
# X-axis is log-scaled
plotAbundanceDensity(tse, layout = "density", assay.type = "relabundance",
                     n = 10 ) +
    scale_x_log10()
                     
# Plots the relative abundance of 10 most abundant taxa as a point plot.
# Point shape is changed from default (21) to 41.
plotAbundanceDensity(tse, layout = "point", assay.type = "relabundance", n = 10,
                     point_shape = 41)
                     
# Plots the relative abundance of 10 most abundant taxa as a point plot.
# In addition to colour, groups can be visualized by size and shape in point plots,
# and adjusted for point size
plotAbundanceDensity(tse, layout = "point", assay.type = "relabundance", n = 10,
                     shape_by = "sex", size_by = "time", point_size=1)

# Ordering via order_descending
plotAbundanceDensity(tse, assay.type = "relabundance", 
                     order_descending = FALSE)

# for custom ordering set order_descending = NA and order the input object
# to your wishes
plotAbundanceDensity(tse, assay.type = "relabundance",
                     order_descending = NA)

microbiome/miaViz documentation built on April 21, 2024, 8:45 a.m.