clustifyr UMAP heatmap wrap — clustifyFun • scMisc

create and save clustifyr UMAP and heatmap

Usage

clustifyFun(
  my_object,
  my_annotations,
  ref_object,
  ref_annotations,
  format,
  ortho = "none",
  filter = FALSE,
  regex = "",
  umap = FALSE,
  width = 10,
  height = 7,
  cluster_rows = TRUE,
  cluster_cols = TRUE,
  cellwidth = 10,
  cellheight = 10,
  fontsize = 10,
  color,
  name
)

Arguments

my_object: query input object
my_annotations: annotations of query input object
ref_object: reference object
ref_annotations: reference annotations
format: format of reference object: possible values are seurat, sc or matrix
ortho: convert to orthologues? Allowed values: none, mouse2human or human2mouse (default: none)
filter: should the reference be filtered? Allowed values: TRUE, FALSE (default: FALSE)
regex: if filter: specify filter term
umap: also create UMAP? Allowed values: TRUE, FALSE (default FALSE)
width: width of heatmap plot (default: 10)
height: height of heatmap plot (default: 7)
cluster_rows: cluster rows? (default: true)
cluster_cols: cluster columns? (default: true)
cellwidth: individual cell width (default: 10)
cellheight: individual cell height (default: 10)
fontsize: fontsize (default: 10)
color: color palette
name: fontsize (default: 10)

Value

save umap/heatmap plot to folder /results/clustifyr/

Examples

if (FALSE) { # \dontrun{
clustifyFun(
    my_object = tcells,
    my_annotations = "cluster",
    ref_object = projectil_til,
    ref_annotations = "functional.cluster",
    format = "seurat",
    ortho = "none",
    height = 25,
    width = 10,
    umap = TRUE,
    color = col_vector,
    name = "projectil_til"
)
} # }