Visualize the NMF basis vectors in a paired heatmap and sequence logo plot

Source: R/viz_basis_vectors.R

The given features matrix is visualized as a heatmap followed by a sequence logo where the positions are aligned for better visualization.

viz_bas_vec_heatmap_seqlogo(
  feat_mat,
  method = "bits",
  pos_lab = NULL,
  add_pseudo_counts = FALSE,
  pdf_name = NULL,
  sinuc_or_dinuc = "sinuc",
  fixed_coord = FALSE
)

viz_bas_vec_seqlogo(
  feat_mat,
  method = "bits",
  pos_lab = NULL,
  add_pseudo_counts = FALSE,
  pdf_name = NULL,
  sinuc_or_dinuc = "sinuc",
  fixed_coord = FALSE
)

viz_bas_vec_heatmap(
  feat_mat,
  pos_lab = NULL,
  add_pseudo_counts = FALSE,
  pdf_name = NULL,
  sinuc_or_dinuc = "sinuc",
  fixed_coord = FALSE
)

Arguments

feat_mat

The features matrix (basis vectors matrix) from archR.
method

For ggseqlogo -- either of "custom", "bits", or "probability". 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.
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.
pdf_name

Name of the file which will be saved as PDF (also provide the extension).
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. Default is FALSE.

Value

nothing

Functions

  • viz_bas_vec_seqlogo: Visualize the NMF basis vectors as a sequence logo

  • viz_bas_vec_heatmap: Visualize the NMF basis vectors as a heatmap

See also

Other visualization functions: plot_ggheatmap(), plot_ggseqlogo(), viz_seqs_acgt_mat_from_seqs()

Examples

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

viz_bas_vec_heatmap_seqlogo(feat_mat = get_clBasVec_m(res,iter=1),
                            sinuc_or_dinuc = "dinuc", fixed_coord = TRUE)

#> Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
#> Scale for 'x' is already present. Adding another scale for 'x', which will
#> replace the existing scale.
#> Coordinate system already present. Adding new coordinate system, which will replace the existing one.
#> Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
#> Scale for 'x' is already present. Adding another scale for 'x', which will
#> replace the existing scale.
#> Coordinate system already present. Adding new coordinate system, which will replace the existing one.
#> Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
#> Scale for 'x' is already present. Adding another scale for 'x', which will
#> replace the existing scale.
#> Coordinate system already present. Adding new coordinate system, which will replace the existing one.

viz_bas_vec_seqlogo(feat_mat = get_clBasVec_m(res,iter=1),
                     sinuc_or_dinuc = "dinuc", fixed_coord = TRUE)

#> Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
#> Scale for 'x' is already present. Adding another scale for 'x', which will
#> replace the existing scale.
#> Coordinate system already present. Adding new coordinate system, which will replace the existing one.
#> Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
#> Scale for 'x' is already present. Adding another scale for 'x', which will
#> replace the existing scale.
#> Coordinate system already present. Adding new coordinate system, which will replace the existing one.
#> Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
#> Scale for 'x' is already present. Adding another scale for 'x', which will
#> replace the existing scale.
#> Coordinate system already present. Adding new coordinate system, which will replace the existing one.

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