********
plotBars
********

======== ===============
plotBars R Documentation
======== ===============

Plot a barplot using ggplot2
----------------------------

Description
~~~~~~~~~~~

Plot a ggplot2 barplot from a matrix or data frame. The data should be
in tabular format (e.g. features in rows and samples in columns).

Usage
~~~~~

.. code:: R

   plotBars(
     data,
     label_x = "Samples",
     label_y = "Abundances",
     label_fill = "Features",
     color = NULL,
     base_size = 11,
     max_scale_value = NULL,
     metadata_groups = NULL
   )

Arguments
~~~~~~~~~

+---------------------+------------------------------------------------+
| ``data``            | Numeric matrix or data frame.                  |
+---------------------+------------------------------------------------+
| ``label_x``         | character Label for the x axis (default        |
|                     | ``"Samples"``).                                |
+---------------------+------------------------------------------------+
| ``label_y``         | character Label for the y axis (default        |
|                     | ``"Abundances"``).                             |
+---------------------+------------------------------------------------+
| ``label_fill``      | character Label for color categories (default  |
|                     | ``"Features"``).                               |
+---------------------+------------------------------------------------+
| ``color``           | Vector with custom colors for the different    |
|                     | features. If empty, the default ggplot2        |
|                     | palette will be used (default ``NULL``).       |
+---------------------+------------------------------------------------+
| ``base_size``       | numeric. Base font size (default ``11``).      |
+---------------------+------------------------------------------------+
| ``max_scale_value`` | numeric. Maximum value to include in the y     |
|                     | axis. By default it is handled automatically   |
|                     | by ggplot2 (default ``NULL``).                 |
+---------------------+------------------------------------------------+
| ``metadata_groups`` | list. Split the plot into groups defined by    |
|                     | the user: list('G1' = c('sample1', sample2'),  |
|                     | 'G2' = c('sample3', 'sample4')) default        |
|                     | ``NULL``).                                     |
+---------------------+------------------------------------------------+

Value
~~~~~

a ggplot2 plot object.

See Also
~~~~~~~~

``plotTaxonomy`` for plotting the most abundant taxa of a SQM object;
``plotHeatmap`` for plotting a heatmap with arbitrary data;
``mostAbundant`` for selecting the most abundant rows in a dataframe or
matrix.

Examples
~~~~~~~~

.. code:: R

   data(Hadza)
   sk = Hadza$taxa$superkingdom$abund
   plotBars(sk, label_y = "Raw reads", label_fill = "Superkingdom")