plot_tfidf: Plot tf-idf results in reduced dimensions

In neurogenomics/scNLP: NLP for Single-cell Omics.

Plot tf-idf results in reduced dimensions

Description

Plot tf-idf enrichment results in reduced dimensional space (e.g. PCA/tSNe/UMAP), Reduced dimensions can be computed based on single-cell data (e.g. RNA expression). .

Usage

plot_tfidf(
  obj,
  reduction = "UMAP",
  label_var = NULL,
  cluster_var = "seurat_clusters",
  replace_regex = "[.]|[_]|[-]",
  terms_per_cluster = 3,
  size_var = 1,
  color_var = "cluster",
  point_alpha = 0.7,
  point_palette = c(unname(pals::alphabet()), rev(unname(pals::alphabet2()))),
  density_palette = "Purples",
  density_adjust = 0.2,
  label_fill = ggplot2::alpha(c("white"), 0.7),
  show_plot = TRUE,
  background_color = "white",
  text_color = "black",
  force = c(0, 1),
  max.overlaps = c(100, 100),
  legend.position = NULL,
  interact = FALSE,
  force_new = FALSE,
  verbose = TRUE,
  ...
)

Arguments

obj	Single-cell data object.
reduction	Name of the reduction to use (case insensitive).
label_var	Which cell metadata column to input to NLP analysis.
cluster_var	Which cell metadata column to use to identify which cluster each cell is assigned to.
replace_regex	Characters by which to split label_var into terms (i.e. tokens) for NLP enrichment analysis.
terms_per_cluster	The maximum number of words to return per cluster.
size_var	Point size variable in obj metadata.
color_var	Point color variable in obj metadata.
point_alpha	Point opacity.
point_palette	Point palette.
density_palette	Density palette.
density_adjust	Density adjust (controls granularity of density plot).
label_fill	Cluster label background color.
show_plot	Whether to print the plot.
background_color	Plot background color.
text_color	Cluster label text color.
force	Force of repulsion between overlapping text labels. Defaults to 1.
max.overlaps	Exclude text labels when they overlap too many other things. For each text label, we count how many other text labels or other data points it overlaps, and exclude the text label if it has too many overlaps. Defaults to 10.
legend.position	the default position of legends ("none", "left", "right", "bottom", "top", "inside")
interact	Whether to make the plot interactive with plotly.
force_new	If NLP results are already detected the metadata, set force_new=TRUE to replace them with new results.
verbose	Whether to print messages.
...	Additional arguments to be passed to ggplot2::geom_point(aes_string(...)).

Examples

data("pseudo_seurat")
obj <- pseudo_seurat
res <- plot_tfidf(obj = obj, 
                  label_var = "celltype", 
                  cluster_var = "cluster")

neurogenomics/scNLP documentation built on Oct. 8, 2024, 5:30 p.m.