Description Usage Arguments Details Value Author(s) Examples
Boxplot
1 | vis_boxplot(obj,group_by)
|
obj |
(required) A data object of class 'ampvis2' (see |
group_by |
(required) Group the samples by a variable in the metadata. |
boxgroup_by |
Group the samples within each boxplot by a variable in the metadata. |
sort_by |
Sort the boxplots by |
normalise |
Can take one of following arguments: (default:
|
plot_type |
Plot type. |
point_size |
The size of points. (default: |
row_show |
The number of variables to show, or a vector of gene/OTU names. (default: |
order_group |
A vector to order the groups by. |
order_boxgroup |
A vector to order the box-groups by. |
title_newline |
Split the facet headers by newline. (default: |
title_size |
Size of text in facet headers. (default: |
plot_flip |
(logical) Flip the axes of the plot axis. (default: |
plot_log |
(logical) Log10-scale the plot. (default: |
adjust_zero |
Keep values of 0 in calculations by adding this value. (default: |
detailed_output |
(logical) Return additional details or not. If |
row_labels |
(mmtravis only) Additional variables in genedata to plot ( |
tax_class |
(ampvis2 only) Converts a specific phylum to class level instead, e.g. |
tax_empty |
(ampvis2 only) How to show OTUs without taxonomic information. One of the following:
|
tax_aggregate |
(ampvis2 only) The taxonomic level to aggregate the OTUs. (default: |
The plot is ordered as one would read a book, from left to right and top to bottom.
A ggplot2 object. If detailed_output = TRUE
a list with a ggplot2 object and additional data.
Thomas Yssing Michaelsen tym@bio.aau.dk
1 2 3 4 5 6 7 8 9 10 11 | ## Not run:
data("example_mmt")
vis_boxplot(example_mmt,
group_by = "Type",
boxgroup_by = "Organism",
row_show = 10,
row_labels = "product",
title_newline = T)
## End(Not run)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.