View source: R/plot_functions.R
multitax_bar_pq | R Documentation |
Note that lvl3 need to be nested in lvl2 which need to be nested in lvl1
multitax_bar_pq(
physeq,
lvl1,
lvl2,
lvl3,
fact = NULL,
nb_seq = TRUE,
log10trans = TRUE
)
physeq |
(required): a |
lvl1 |
(required) Name of the first (higher) taxonomic rank of interest |
lvl2 |
(required) Name of the second (middle) taxonomic rank of interest |
lvl3 |
(required) Name of the first (lower) taxonomic rank of interest |
fact |
Name of the factor to cluster samples by modalities.
Need to be in |
nb_seq |
(logical; default TRUE) If set to FALSE, only the number of ASV is count. Concretely, physeq otu_table is transformed in a binary otu_table (each value different from zero is set to one) |
log10trans |
(logical, default TRUE) If TRUE, the number of sequences (or ASV if nb_seq = FALSE) is log10 transformed. |
A ggplot2 graphic
Adrien Taudière
if (requireNamespace("ggh4x")) {
multitax_bar_pq(data_fungi_sp_known, "Phylum", "Class", "Order", "Time")
multitax_bar_pq(data_fungi_sp_known, "Phylum", "Class", "Order")
multitax_bar_pq(data_fungi_sp_known, "Phylum", "Class", "Order",
nb_seq = FALSE, log10trans = FALSE
)
}
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