plotSeries {miaViz} | R Documentation

## Plot Series

### Description

This function plots series data.

### Usage

    plotSeries(
      object,
      x,
      y = NULL,
      rank = NULL,
      colour_by = NULL,
      size_by = NULL,
      linetype_by = NULL,
      abund_values = "counts",
      ...
    )

    ## S4 method for signature 'SummarizedExperiment'
    plotSeries(
      object,
      x,
      y = NULL,
      rank = NULL,
      colour_by = NULL,
      size_by = NULL,
      linetype_by = NULL,
      abund_values = "counts",
      ...
    )

### Arguments

`object` | a `SummarizedExperiment` object.
`x` | a single character value for selecting the column from `ColData` that will specify values of x-axis.
`y` | a single character value for selecting the taxa from `rownames`. This parameter specifies taxa whose abundances will be plotted.
`rank` | a single character value defining a taxonomic rank, that is used to agglomerate the data. Must be a value of `taxonomicRanks()` function.
`colour_by` | a single character value defining a taxonomic rank, that is used to color plot. Must be a value of `taxonomicRanks()` function.
`size_by` | a single character value defining a taxonomic rank, that is used to divide taxa to different line size types. Must be a value of `taxonomicRanks()` function.
`linetype_by` | a single character value defining a taxonomic rank, that is used to divide taxa to different line types. Must be a value of `taxonomicRanks()` function.
`abund_values` | a single character value for selecting the `assay` to be plotted. (default: `abund_values = "counts"`)
`...` | additional parameters for plotting. See `mia-plot-args` for more details i.e. call `help("mia-plot-args")`

### Details

This function creates series plot, where x-axis includes e.g. time points, and y-axis abundances of selected taxa.

### Value

A `ggplot2` object

### Author(s)

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

### Examples

    library(mia)
    object <- microbiomeDataSets::SilvermanAGutData()
    # Plots 2 most abudant taxa, which are colore by their family
    plotSeries(object,
               x = "DAY_ORDER",
               y = getTopTaxa(object, 2),
               colour_by = "Family")

    # Counts relative abundances
    object <- transformCounts(object, method = "relabundance")

    # Selects taxa
    taxa <- c("seq_1", "seq_2", "seq_3", "seq_4", "seq_5")

    # Plots relative abundances of phylums
    plotSeries(object[taxa,],
               x = "DAY_ORDER",
               colour_by = "Family",
               linetype_by = "Phylum",
               abund_values = "relabundance")

    # In addition to 'colour_by' and 'linetype_by', 'size_by' can also be used to group taxa.
    plotSeries(object,
               x = "DAY_ORDER",
               y = getTopTaxa(object, 5),
               colour_by = "Family",
               size_by = "Phylum",
               abund_values = "counts")

[Package miaViz version 1.2.1 Index]