plot_feature: Plot cells in reduced dimensionality 2D space

Description Usage Arguments

View source: R/plots.R

Description

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

Usage

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plot_feature(fce, feature = NULL, expt = "sce", method = "UMAP",
  plot_dat = NULL, pt_size = 0.01, pt_alpha = 1,
  label_text = FALSE, label_size = 6, label_color = "grey",
  .cols = NULL, cell_filter = NULL, palette_type = "cloupe",
  col_pal = "Reds", max_y = NULL, plot_title = NULL,
  dims_to_plot = c(1, 2))

Arguments

fce

fce object of class MultiAssayExperiment

feature

single feature to plot, either gene name or column in colData

expt

Data type to use for plot, one of either sce (rna data, the default) or fsce (functional data). Defaults to "sce"

method

dimensionality reduction for plotting. defaults to UMAP

plot_dat

supplemental data.frame containing feature to plot. Must have a column named cell that contains matching colnames in colData

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

.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

plot_title

string to supply for title for the plot, otherwise title is the feature

dims_to_plot

number of dimensions


hesselberthlab/scrunchy documentation built on Dec. 11, 2018, 1:30 a.m.