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))
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
)
matrix from input graph, with labels propagated
edge vertices of igraph graph object
edge weights of igraph graph object
gene count matrix
boolean Whether label is fixed
integer Maximal number of iterations (default=10)
numeric Constant used for diffusion on the graph, exp(-diffusion.fading * (edge_length + diffusion.fading.const)) (default=1.0)
numeric Another constant used for diffusion on the graph, exp(-diffusion.fading * (edge_length + diffusion.fading.const)) (default=0.1)
numeric Absolute tolerance as a stopping criteria (default=1e-3)
boolean Verbose mode (default=TRUE)
boolean Whether to normalize values (default=FALSE)