Plot Feature — plot_feature • seuratTools

Plots gene or transcript expression overlaid on a given embedding. If multiple features are supplied the joint density of all features will be plotted using Nebulosa

plot_feature(
  seu,
  embedding = c("umap", "pca", "tsne"),
  features,
  dims = c(1, 2),
  return_plotly = FALSE,
  pt.size = 1
)

Arguments

seu: A Seurat object
embedding: Dimensional reduction technique to be used
features: Features to plot
dims: Dimensions to plot, must be a two-length numeric vector

Examples


# static, single feature
plot_feature(human_gene_transcript_seu, embedding = "umap", features = c("NRL"), return_plotly = FALSE)
#> Warning: partial match of 'just' to 'justification'

# static, multi-feature
plot_feature(human_gene_transcript_seu, embedding = "umap", features = c("RXRG", "NRL"), return_plotly = FALSE)
#> Warning: The following requested variables were not found: RXRG
#> Error in .extract_feature_data(exp_data, features): 'RXRG' feature(s) not present in meta.data or expression data
# interactive, multi-feature
plotly_plot <- plot_feature(human_gene_transcript_seu, embedding = "umap", features = c("RXRG", "NRL"))
#> Warning: The following requested variables were not found: RXRG
#> Error in .extract_feature_data(exp_data, features): 'RXRG' feature(s) not present in meta.data or expression data
print(plotly_plot)
#> Error in eval(expr, envir, enclos): object 'plotly_plot' not found