Description Usage Arguments Examples
This is a function for plotting log2 fold change.
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phyloseq |
A phyloseq object contain otu table, taxonomy table, sample metadata and phylogenetic tree, or a phyloseq object only contain constructed OTU table and metadata. |
feature |
The column name of the feature you want to from metadata, e.g. "Phenotype". |
level |
Which taxonomy level to calculate fold change. Default is NA. If level is given, will use construct_otu_table function to construct OTU table, and use DESeq to calculate fold change. |
p_value |
The cut off P value for the fold change. Default is 0.05. |
save_res |
Default is FALSE. If TRUE, will save original result DESeq2_result.rds to current working directory. |
reference |
The control group. Default is NA. |
treatment |
The treatment group. Default is NA. |
print_to_screen |
Default is FALSE. If TRUE, print fold change table to the screen. |
1 | log2fc(demo_phyloseq_object, feature = "diagnosis", level = "Genus")
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