plot_feature: Plot cells in reduced dimensionality 2D space

In rnabioco/scbp: Boilerplate functions for single cell rna-seq analysis

Plot cells in reduced dimensionality 2D space

Description

Cells can be colored by gene or feature in meta.data dataframe

See also plot_feature group argument

Usage

plot_feature(
  seurat_obj,
  feature = NULL,
  plot_dat = NULL,
  pt_size = 0.001,
  pt_alpha = 1,
  label_text = FALSE,
  label_size = 6,
  label_color = NULL,
  .cols = NULL,
  cell_filter = NULL,
  palette_type = "cloupe",
  col_pal = "Reds",
  max_y = NULL,
  legend_title = NULL,
  embedding = "tsne",
  show_negative = FALSE,
  minimal_theme = FALSE,
  group = NULL,
  group_rows = NULL,
  group_cols = NULL,
  dims = c(1, 2),
  sorted = c("by_feature", "none", "random"),
  transform = "identity",
  na_col = "grey",
  ggrepel_opts = list(),
  highlight = NULL
)

plot_umap(seurat_obj, ...)

plot_tsne(seurat_obj, ...)

plot_pca(seurat_obj, ...)

plot_harmony(seurat_obj, ...)

plot_features_split(
  seurat_obj,
  feature,
  group = "orig.ident",
  embedding = "umap",
  cols = NULL,
  ...
)

Arguments

seurat_obj	seurat object
feature	feature to plot
plot_dat	supplemental data.frame containing feature to plot. Must have a column named cell that contains matching colnames in seurat_obj@data
pt_size	size of points produced by geom_point
pt_alpha	alpha value for points plotted by geom_point
label_text	if TRUE display feature labels on plot
label_size	size of label text
label_color	color of label text, defaults to same colors as feature
.cols	vector of colors to use for plot.
cell_filter	character vector of cell names to include in plot
palette_type	color palette type to use (either viridis, brewer, or cloupe) defaults to using cellranger loupe-like colors
col_pal	palette name to use if palette_type is brewer
max_y	maximum feature value to set scale to. Defaults to max of the feature
legend_title	string to supply for title for the legend
embedding	dimensionality reduction to use for plotting
show_negative	By default the legend value for continuous features will be clipped at zero. If false, then the minumum value for the plotted feature will be used.
minimal_theme	plot bare minimum
group	grouping varible to split plots
group_rows	number of rows of plots when faceting by group (defaults to NULL)
group_cols	number of cols of plots when faceting by group
dims	which dims to plot from embedding, defaults to first and second, i.e. c(1,2).
sorted	should the plotting be determined by sorting in ascending order? Default is sorted by_feature (one of "by_feature", "none", "random")
transform	adrgument o be passed to scale_color_gradientn for continuous data. defaults to no transformation (i.e. "identity") See ?continous_scale for available transforms.
na_col	Color for NA values (default = "grey")
ggrepel_opts	named list of options to pass to ggrepel geom_text_repel.
highlight	individual values to highlight from a metadata annotation selected for plotting. other values will be set to 'na_col'.
...	Additional parameters to pass to plot_feature
cols	vector of cols to identity class, used to keep consistent colors between plots
add_title	want a title?
...	additional args passed to plot_feature

rnabioco/scbp documentation built on July 7, 2023, 10:10 p.m.