psmelt_samples_pq {MiscMetabar} | R Documentation |
Build a sample information tibble from physeq object
Description
Hill numbers are the number of equiprobable species giving the same diversity value as the observed distribution.
Note that contrary to hill_pq()
, this function does not take into
account for difference in the number of sequences per samples/modalities.
You may use rarefy_by_sample = TRUE if the mean number of sequences per
samples differs among modalities.
Usage
psmelt_samples_pq(
physeq,
hill_scales = c(0, 1, 2),
filter_zero = TRUE,
rarefy_by_sample = FALSE,
taxa_ranks = NULL
)
Arguments
physeq |
(required): a |
hill_scales |
(a vector of integer) The list of q values to compute the hill number H^q. If Null, no hill number are computed. Default value compute the Hill number 0 (Species richness), the Hill number 1 (exponential of Shannon Index) and the Hill number 2 (inverse of Simpson Index). |
filter_zero |
(logical, default TRUE) Do we filter non present OTU from samples ? For the moment, this has no effect on the result because the dataframe is grouped by samples with abundance summed across OTU. |
rarefy_by_sample |
(logical, default FALSE) If TRUE, rarefy
samples using |
taxa_ranks |
A vector of taxonomic ranks. For examples c("Family","Genus"). If taxa ranks is not set (default value = NULL), taxonomic information are not present in the resulting tibble. |
Value
A tibble with a row for each sample. Columns provide information
from sam_data
slot as well as hill numbers, Abundance (nb of sequences),
and Abundance_log10 (log10(1+Abundance)).
Author(s)
Adrien Taudière
Examples
if (requireNamespace("ggstatsplot")) {
psm_tib <- psmelt_samples_pq(data_fungi_mini, hill_scales = c(0, 2, 7))
ggstatsplot::ggbetweenstats(psm_tib, Height, Hill_0)
ggstatsplot::ggbetweenstats(psm_tib, Height, Hill_7)
psm_tib_tax <- psmelt_samples_pq(data_fungi_mini, taxa_ranks = c("Class", "Family"))
ggplot(filter(psm_tib_tax, Abundance > 2000), aes(y = Family, x = Abundance, fill = Time)) +
geom_bar(stat = "identity") +
facet_wrap(~Height)
}