View source: R/beta_div_test.R
plot_LCBD_pq | R Documentation |
A wrapper for the adespatial::beta.div()
function in the case of physeq
object.
plot_LCBD_pq(
physeq,
p_adjust_method = "BH",
pval = 0.05,
sam_variables = NULL,
only_plot_significant = TRUE,
...
)
physeq |
(required): a |
p_adjust_method |
(chr, default "BH"): the method used to adjust p-value |
pval |
(int, default 0.05): the value to determine the significance of LCBD |
sam_variables |
A vector of variables names present in the |
only_plot_significant |
(logical, default TRUE) Do we plot all LCBD values or only the significant ones |
... |
Others arguments passed on to |
This function is mainly a wrapper of the work of others.
Please make a reference to vegan::beta.div()
if you
use this function.
A ggplot2 object build with the package patchwork
Adrien Taudière
LCBD_pq, adespatial::beta.div()
data(data_fungi)
if (requireNamespace("adespatial")) {
plot_LCBD_pq(data_fungi_mini,
nperm = 100, only_plot_significant = FALSE,
pval = 0.2
)
}
if (requireNamespace("adespatial")) {
plot_LCBD_pq(data_fungi_mini,
nperm = 100, only_plot_significant = TRUE,
pval = 0.2
)
if (requireNamespace("patchwork")) {
plot_LCBD_pq(data_fungi_mini,
nperm = 100, only_plot_significant = FALSE,
sam_variables = c("Time", "Height")
)
plot_LCBD_pq(data_fungi_mini,
nperm = 100, only_plot_significant = TRUE, pval = 0.2,
sam_variables = c("Time", "Height", "Tree_name")
) &
theme(
legend.key.size = unit(0.4, "cm"),
legend.text = element_text(size = 10),
axis.title.x = element_text(size = 6)
)
}
}
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