Description Usage Arguments Examples
This is a function for stacked barplot. PS: When faceting the stacked bar plot, use facet_wrap( vars(column_name), scales = "free_x")
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phyloseq |
A phyloseq object contain otu table, taxonomy table, sample metadata and phylogenetic tree. Set it to NULL if using an OTU table and metadata to draw the stacked barplot. |
level |
A taxonomy level to plot stacked bar. Default is NA. Required when using phyloseq object. |
feature |
The feature that will show as a colorbar under x axis. Default is NA. |
otu_table |
An OTU table. Taxa are colnames, SampleID are rownames (just like phyloseq). Set it to NULL if using phyloseq. |
metadata |
A metadata for the OTU table. SampleID are rownames (just like phyloseq). Set it to NULL if using phyloseq. |
order |
A vector of arranged SampleID in wanted order. Default is NULL. If NULL, plot_stacked_bar will automatically arrange samples by the most abundance taxonomy in decreasing order. |
relative_abundance |
Turn plot into relative abundance or not. Default is TRUE. |
legend_position |
Legend position. Default is "top". legend_position should be one of "none", "left", "right", "bottom", "top". |
colors |
A vector of colors. The number of colors should be larger than the number of level. Default is NULL, if NULL, plot_stacked_bar will use distinctive_colors for the plot. |
collapse |
Default is 0.01, collapse taxonomy which abundance is lower than 1 percent of total into "Others". Set it to FALSE if want to show all taxonomy levels. |
title |
Default is NA, value for ggplot2::labs(title). |
x_text_angle |
Default is 90, value for ggplot2::ggplot(themt(axis.text.x = element_text( angle))). |
1 2 | # Minimum usage
plot_stacked_bar(demo_phyloseq_object, level = "Genus")
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