Plot the top phenotypes

Source: R/get_top_phenos.R, R/get_top_phenotypes.R

Create a radar chart of the phenotypes with the highest loadings for each reduction factor.

Create a radar chart of the phenotypes with the highest loadings for each reduction factor.

get_top_phenotypes(
  obj,
  metadata = NULL,
  reduction = NULL,
  n_phenotypes = 3,
  factors_plot = 1:10,
  invert_vars = FALSE,
  show_plot = TRUE,
  title = NULL,
  x = "phenotype",
  y = "loading",
  verbose = TRUE
)

get_top_phenotypes(
  obj,
  metadata = NULL,
  reduction = NULL,
  n_phenotypes = 3,
  factors_plot = 1:10,
  invert_vars = FALSE,
  show_plot = TRUE,
  title = NULL,
  x = "phenotype",
  y = "loading",
  verbose = TRUE
)

Arguments

obj

Seurat object or dimensionality reduction object.
metadata

Phenotype metadata. Not needed if obj is a Seurat object.
reduction

Reduction to use. If NULL, defaults to first available reduction.
n_phenotypes

Number of top phenotypes per reduction factor to select.
invert_vars

Switch the axes of factors and loadings in plot.
show_plot

Whether to print the plot or simply return it.
title

Plot title.
x

x-axis variable.
y

y-axis variable.
verbose

Print messages.
seurat

Seurat object or Seurat::DimReducObject.

Value

data.table of top phenotypes

data.table of top phenotypes

Examples

data("DEGAS_seurat")
top_phenos <- get_top_phenotypes(seurat = DEGAS_seurat)

#> Error in get_top_phenotypes(seurat = DEGAS_seurat): unused argument (seurat = DEGAS_seurat)
data("DEGAS_seurat")
top_phenos <- get_top_phenotypes(obj = DEGAS_seurat)

#> Extracting embeddings from Seurat reduction:  contributionGene