smooth_count_matrix {sccore}

Smooth gene expression, used primarily within conos::correctGenes. Used to smooth gene expression values in order to better represent the graph structure. Use diffusion of expression on graph with the equation dv = exp(-a * (v + b))

Description

Smooth gene expression, used primarily within conos::correctGenes. Used to smooth gene expression values in order to better represent the graph structure. Use diffusion of expression on graph with the equation dv = exp(-a * (v + b))

Usage

smooth_count_matrix(
  edge_verts,
  edge_weights,
  count_matrix,
  is_label_fixed,
  max_n_iters = 10L,
  diffusion_fading = 1,
  diffusion_fading_const = 0.1,
  tol = 0.001,
  verbose = TRUE,
  normalize = FALSE
)

Arguments

edge_verts

edge vertices of igraph graph object

edge_weights

edge weights of igraph graph object

count_matrix

gene count matrix

is_label_fixed

boolean Whether label is fixed

max_n_iters

integer Maximal number of iterations (default=10)

diffusion_fading

numeric Constant used for diffusion on the graph, exp(-diffusion.fading * (edge_length + diffusion.fading.const)) (default=1.0)

diffusion_fading_const

numeric Another constant used for diffusion on the graph, exp(-diffusion.fading * (edge_length + diffusion.fading.const)) (default=0.1)

tol

numeric Absolute tolerance as a stopping criteria (default=1e-3)

verbose

boolean Verbose mode (default=TRUE)

normalize

boolean Whether to normalize values (default=FALSE)

Value

matrix from input graph, with labels propagated