viz_bas_vec: Visualize the NMF basis vectors

In snikumbh/seqArchR: Identify Different Architectures of Sequence Elements

Visualize the NMF basis vectors

Description

The given features matrix is visualized as a paired heatmap and sequence logo where the positions are aligned for better visualization., or as a single heatmap or as a single sequence logo.

Usage

viz_bas_vec(
  feat_mat,
  ptype = c("heatmap", "seqlogo"),
  method = "bits",
  pos_lab = NULL,
  pdf_name = NULL,
  add_pseudo_counts = FALSE,
  sinuc_or_dinuc = "sinuc",
  fixed_coord = FALSE
)

Arguments

feat_mat	The features matrix (basis vectors matrix) from seqArchR.
ptype	Character vector of length one or two. Specify just one of "heatmap" or "seqlogo" to visualize the basis vectors as such, or specify a vector of length two for plotting both, heatmap and seqlogo. These are then arranged one below the other, the first on top and the second under it.
method	Specify either of "custom", "bits", or "probability" for plotting sequence logo. Default is "bits".
pos_lab	Labels for sequence positions, should be of same length as that of the sequences. Default value is NULL, when the positions are labeled from 1 to the length of the sequences.
pdf_name	Filename to save the plot, also provide the extension.
add_pseudo_counts	Logical, taking values TRUE or FALSE, default set to FALSE. Setting it to TRUE will enable adding pseudo-counts to the features matrix.
sinuc_or_dinuc	"sinuc" or "dinuc" for choosing between mono- and dinucleotide profiles respectively.
fixed_coord	Set this to TRUE to use a fixed aspect ratio for the plot irrestive of the width and height of the PDF. Default is FALSE.

Value

nothing

See Also

Other visualization functions: viz_pwm(), viz_seqs_acgt_mat()

Examples

res <- readRDS(system.file("extdata", "example_seqArchRresult.rds",
         package = "seqArchR", mustWork = TRUE))

# Visualize basis vectors at iteration 1 of seqArchR result as heatmap and
# sequence logo
viz_bas_vec(feat_mat = get_clBasVec_m(res,iter=1), sinuc_or_dinuc = "dinuc",
                ptype = c("heatmap", "seqlogo"))


# Visualize basis vectors at iteration 1 of seqArchR result as sequence logos
viz_bas_vec(feat_mat = get_clBasVec_m(res,iter=1), ptype = "seqlogo",
                 sinuc_or_dinuc = "dinuc")


# Visualizing basis vector for a single cluster as a heatmap
viz_bas_vec(feat_mat = as.matrix(get_clBasVec_m(res,iter=1)[,3]),
                 ptype = "heatmap", sinuc_or_dinuc = "dinuc")

snikumbh/seqArchR documentation built on March 11, 2024, 7:06 p.m.