HotLoadings.plot_loadings_simple: HotLoadings.plot_loadings_simple Plot Loadings the simple way

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

Description

HotLoadings.plot_loadings_simple Plot Loadings the simple way

Usage

HotLoadings.plot_loadings_simple(
  PSOBJ,
  format = c("short", "last", "long", "none"),
  data.splsda,
  method = "mean",
  contrib = "max",
  Y_name,
  comp,
  ndisplay = 15,
  offset = 0.005,
  colors = 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.
method	a character set to 'mean' or 'median' indicating the criterion to assess the contribution. We recommend using median in the case of count or skewed data.
contrib	a character set to 'max' or 'min' indicating if the color of the bar should correspond to the group with the maximal or minimal expression levels / abundance.
Y_name	A character string indicating which is the variable associated with component specified. Must be a dicothomous variable.
comp	integer value indicating the component of interest from the object.
ndisplay	integer indicating how many of the most important variables are to be plotted (ranked by decreasing weights in each PLS-component). Useful to lighten a graph.
offset	A value indicating the amount of justification from axis for possible plots. (Default = 0.005)
colors	Vector of Hexadecimal codes for colors. Must be the same length of Y levels.

Value

The function return a ggplot2 loadings object.

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