pseudotime.knetl {iCellR}

iCellR KNN Network

Description

This function takes an object of class iCellR and and runs kNet for dimensionality reduction.

Usage

pseudotime.knetl(
  x = NULL,
  dist.method = "euclidean",
  k = 5,
  abstract = TRUE,
  data.type = "pca",
  dims = 1:20,
  conds.to.plot = NULL,
  my.layout = "layout_with_fr",
  node.size = 10,
  cluster.membership = FALSE,
  interactive = TRUE,
  node.colors = NULL,
  edge.color = "gray",
  out.name = "Pseudotime.Abstract.KNetL",
  my.seed = 1
)

Arguments

x

An object of class iCellR.

dist.method

the distance measure to be used to compute the dissimilarity matrix. This must be one of: "euclidean", "maximum", "mandatattan", "canberra", "binary", "minkowski" or "NULL". By default, distance="euclidean". If the distance is "NULL", the dissimilarity matrix (diss) should be given by the user. If distance is not "NULL", the dissimilarity matrix should be "NULL".

k

KNN the higher the number the less sensitivity, default = 5.

abstract

Draw all the cells or clusters, , default = TRUE.

data.type

Choose between "tsne", "pca", "umap", default = "pca". We highly recommend PCA.

dims

PCA dimentions to be use for clustering, default = 1:20.

conds.to.plot

Choose the conditions you want to see in the plot, default = NULL (all conditions).

my.layout

Choose a layout, default = "layout_with_fr".

node.size

Size of the nodes, , default = 10.

cluster.membership

Calculate memberships based on distance.

interactive

If set to TRUE an interactive HTML file will be created, default = TRUE.

node.colors

Color of the nodes, default = random colors.

edge.color

Solor of the edges, default = "gray".

out.name

If "interactive" is set to TRUE, the out put name for HTML, default = "Abstract.KNetL".

my.seed

seed number, default = 1.

Value

A plot.