layout_2d: Force-directed layout
In JiekaiLab/SOT: Single-cell Orientation Tracing

2-D visualization of data on kNN graph using force-directed layout

layout_2d(
  sce,
  usedEmbed = "PCA",
  usedDims = NULL,
  datatype = NULL,
  filename = NULL,
  k = 35,
  n_trees = 50,
  max_iter = 2,
  seed = 1,
  layout_method = "FR",
  grid = "auto",
  iterations = 1000,
  repel = 2,
  plotstep = 0,
  clus_method = NULL,
  shape = NULL,
  colour_condition = NULL,
  colour_gene = NULL,
  colour_embed = NULL,
  color_scale = NULL,
  cmap = NULL,
  compute_layout = TRUE,
  orderExp = FALSE,
  title = NULL,
  ncol = NULL,
  nrow = NULL,
  alpha = 0.9,
  size = 1,
  width = 4,
  height = 3,
  rmelements = NULL,
  ...
)

`sce`	A SingleCellExperiment object.
`usedEmbed`	Specify the reduce dimension type for construct network. See current avaible embedding by `reducedDimNames`.
`usedDims`	A vector to specify particular dimensions in usedEmbed to calculate.
`datatype`	Type of expression.
`filename`	Filename to save - default is NULL.
`k`	k nearest neighbors to construct graph.
`n_trees`	Number of trees for largeVis.
`max_iter`	max_iter for largeVis. see `randomProjectionTreeSearch`
`seed`	Random seed.
`layout_method`	Graph layout method, can be one of FR, largeVis or umap.
`grid`	Character scalar, whether to use the faster, but less accurate grid based implementation of the algorithm. By default (“auto”), the grid-based implementation is used if the graph has more than one thousand vertices.
`iterations`	Iterations number of iterations to be performed.
`repel`	The repel constant: the greater the constant k the stronger the repulsion force between points.
`plotstep`	Plot step.
`clus_method`	Clustering method besed on graph.
`colour_condition`	Label the cells with continuous color.
`colour_gene`	A character of a vector of a gene expression.
`colour_embed`	A character of a reduced dimentsion.
`color_scale`	Scatter plot color correponding to levels - default is NULL.
`cmap`	Color style of cmap will be used when color_scale is NULL.
`compute_layout`	Compute fr layout or not. If compute_layout is FASLE, uese the usedEmbed as layout.
`orderExp`	Order plot to highlight high expressed cells.
`title`	Plot title.
`ncol`	(optional) number of columns in the plot grid.
`nrow`	(optional) number of rows in the plot grid.
`alpha`	Transparency of points.
`size`	Point size.
`width`	Width of the figure.
`height`	Height of the figure.
`rmelements`	A vector of elememts to be removed rremove.
`...`	Additional arguments passed on to `umap`