Violin plot of single cell gene expression — expression.Plot • scMiko

Draws violin plot of single cell data, stratified by specified group. Hierarchically-clustered dendrogram is overlaid to illustrate relationships between groups.

expression.Plot(
  so,
  which.gene,
  e.mat = NULL,
  f.mat = NULL,
  which.group = "seurat_clusters",
  which.data = "data",
  which.assay = DefaultAssay(so),
  x.label = NULL,
  x.label.angle = NULL,
  show.violin = T,
  show.full.axis = T,
  font.size = NULL,
  verbose = T
)

Arguments

so: Seurat object
which.gene: query gene. Must be available in Seurat object.
e.mat: expression matrix (gene x cell). If not provided, computed from seurat object (more computationally heavy).
f.mat: expression fraction matrix (gene x cell). If not provided, computed from seurat object (more computationally heavy).
which.group: Group to cluster gene expression by. Must be column header in so meta data. Default is "seurat_clusters".
which.data: Specifies which seurat data used to compute e.mat and f.mat. Must be either "data" (default) or "scale". Used only if e.mat and f.mat are not provided.
which.assay: Specifies which seurat assay to used to compute e.mat. Used only if e.mat is not provided. Default is DefaultAssay(so)
x.label: x axis title (a character). Default is which.group.
x.label.angle: rotation angle for x axis title (a numeric). Default is NULL.
show.violin: Show expression as violin plot. Default is T.
show.full.axis: Show full normalized axis [0,1], rather than adapting to data. Default is T.
font.size: Size of font.
verbose: print progress. Default is T.

Value

ggplot object

Examples


# get expression plot of GPNMB stratified by cluster group.
plt.sgExp.clust <- expression.Plot.dev(so.query, which.gene = "GPNMB", which.group = "seurat_clusters", which.data = "data")
#> Error in expression.Plot.dev(so.query, which.gene = "GPNMB", which.group = "seurat_clusters",     which.data = "data"): could not find function "expression.Plot.dev"
print(plt.sgExp.clust)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'print': object 'plt.sgExp.clust' not found