HotLoadings.heat_map: Plot Heatmap the short way

In mcalgaro93/HotLoadings: HotLoadings: a fancy way to plot mixOmics loadings and heatmaps

Description

The user need to be at the end of mixOmics pipeline.

Usage

HotLoadings.heat_map(
  PSOBJ,
  format = c("short", "last", "long", "none"),
  data.splsda,
  Y_name,
  component,
  n_top = 15,
  sample_name,
  offset = 0.005,
  order = TRUE,
  facet_formula = NULL
)

Arguments

PSOBJ	A phyloseq object.
format	"last" if only the deepest taxonomic characterization is needed. "long" if all taxonomic levels are needed. "short" if last 2 known taxonomic levels are needed. "none" for the SV/OTU number only.
data.splsda	A sPLS-DA object from mixomics.
Y_name	A character string indicating which is the variable associated with component specified. Must be a dicothomous variable.
component	A character string containing sPLS-DA's component name.
n_top	An integer number indicating how many top associated features to keep. (Default = 15)
sample_name	A character string indicating which is the variable with sample names.
offset	A value indicating the amount of justification from axis for possible plots. (Default = 0.005)
order	A boolean value indicating if the loadings should be separately ordered by positives and negatives (Default = TRUE). If FALSE loadings are ordered using their absolute value.
facet_formula	A formula for facetting (default is NULL).

Value

The function plots heatmap for n_top features in rows and samples in columns.

See Also

HotLoadings.plot_loadings_long or HotLoadings.plot_loadings to plot loadings.

mcalgaro93/HotLoadings documentation built on June 13, 2021, 10:01 p.m.