Heatmap of Phosphopeptides Grouped by Cluster

Creates a large phosphopeptide heatmap colored by signal intensity, grouped by consensus cluster with high-contrast cluster color bars. Supports custom row ordering and optional legend/heatkey output files.

Usage

graph.ptm.by.cluster(
  ptmtable,
  common.clusters,
  filename = "ptm_by_cluster_heatmap.pdf",
  legend.filename = NULL,
  heatkey.filename = NULL,
  cluster.order = names(common.clusters),
  order.rows = c("as.is", "mean", "slope", "hclust"),
  cluster.cols = FALSE,
  zlim = 3,
  min.shared = 2,
  show.row.labels = FALSE,
  show.col.labels = TRUE,
  row_cex = 0.2,
  col_cex = 0.8,
  main = "Phosphopeptides grouped by cluster"
)

Arguments

ptmtable

A numeric matrix with PTMs as rows and samples as columns.

common.clusters

A named list where each element is a character vector of PTM identifiers belonging to that cluster.

filename

Output filename for the main heatmap PDF. Defaults to "ptm_by_cluster_heatmap.pdf".

legend.filename

Optional filename for a separate PDF cluster legend. If NULL, no legend file is written.

heatkey.filename

Optional filename for a separate PDF color scale key. If NULL, no heatkey file is written.

cluster.order

Character vector specifying the order in which clusters are displayed. Defaults to names(common.clusters).

order.rows

Method to order rows within clusters: "as.is" (no reordering), "mean" (by row-wise mean), "slope" (by linear trend), or "hclust" (hierarchical clustering). Defaults to "as.is".

cluster.cols

Logical; if TRUE, columns are also hierarchically clustered. Defaults to FALSE.

zlim

Numeric; the upper/lower limit for the heatmap color scale (values are clipped to [-zlim, zlim]). Defaults to 3.

min.shared

Minimum number of shared finite values required to compute distance between two samples. Defaults to 2.

show.row.labels

Logical; show row labels (PTM identifiers). Defaults to FALSE.

show.col.labels

Logical; show column labels (sample names). Defaults to TRUE.

row_cex

Character expansion factor for row labels. Defaults to 0.2.

col_cex

Character expansion factor for column labels. Defaults to 0.8.

main

Plot title. Defaults to "Phosphopeptides grouped by cluster".

Value

Invisibly returns a list containing:

• mat: The clustered expression matrix.

• blocks: List of ordered sub-matrices, one per cluster.

• rowsep: Row indices separating clusters.

• cluster.palette: Named vector of cluster colors.

Examples

if (FALSE) { # \dontrun{
res <- graph.ptm.by.cluster(
  ptmtable = ptmtable,
  common.clusters = common.clusters,
  filename = "ptm_heatmap.pdf",
  order.rows = "hclust"
)
} # }