phy_heatmap: Heatmap of microbiota features, NOT EXPORTED, because I...
In g-antonello/gautils2: Wrapper of my functions to wrangle mostly microbiome data

phy_heatmap

R Documentation

Heatmap of microbiota features, NOT EXPORTED, because I haven't tested it yet!!

Description

Make a quick heatmap of selected features, also transforming internally

Usage

phy_heatmap(
  physeq,
  variable,
  physeq_transformation = "identity",
  taxa = "all",
  aggregation_samples = "median",
  taxa_into_rows = TRUE,
  scale = "row",
  add_sample_size = TRUE,
  angle_col = "90",
  legend = FALSE,
  treeheight_row = 20,
  treeheight_col = 20,
  legend_labels = NULL
)

Arguments

`physeq`	A phyloseq object
`variable`	The variable to consider for clustering
`physeq_transformation`	The transformation you want to apply to your data. Default is `identity`, which is no transformation
`taxa`	A facultative list of taxa to subset the phyloseq by. Default is `all`
`aggregation_samples`	If you want to perform variable-wise aggregation. the allowed aggregation methods here are `mean, median, none`. NB: `none` doesn't work yet
`taxa_into_rows`	A `logical`. It asks whether you want taxa as rows or columns of the heatmap. make sure you do the scaling right, then, in the next parameter
`scale`	The `scale` option in `pheatmap`, either scale by row or column. default is "row", as also `taxa_into_rows` default is TRUE
`add_sample_size`	A `logical`. It asks whether you want to add the per-category sample size in your variable's labels
`angle_col`	A `numeric/character` value of the degrees of tilting of labels. Justification is taken care of automatically
`legend`	A `logical`. It asks whether you want to draw the legend or not
`treeheight_row`	A `numeric` value for drawing the height of the row-wise tree clustering
`treeheight_col`	A `numeric` value for drawing the height of the column-wise tree clustering
`legend_labels`	A `character` vector of length 3 that describes the 3 labels to print on the legend. These labels will be printed as bottom, middle, top

Value

A pheatmap plot object. you can convert it into a ggplot2 object (to some extent) with pheatmap_ggplot <- ggplotify::as.ggplot(returned_pheatmap_object)[[2]]

Examples

data(enterotype)

phy_heatmap(physeq = enterotype,
            variable = "SeqTech",
            aggregation_samples = "median",
            taxa_into_rows = TRUE,
            scale = "row",
            add_sample_size = TRUE,
            angle_col = 45,
            legend = FALSE)

g-antonello/gautils2 documentation built on Nov. 28, 2022, 9:39 a.m.