ssvSignalHeatmap.ClusterBars {seqsetvis}R Documentation

heatmap style representation of membership table. instead of clustering, each column is sorted starting from the left.

Description

Compared to ssvSignalHeatmap, cluster_bars are displayed on the left once instead of for each facet

Usage

ssvSignalHeatmap.ClusterBars(
  bw_data,
  nclust = 6,
  perform_clustering = c("auto", "yes", "no")[1],
  row_ = "id",
  column_ = "x",
  fill_ = "y",
  facet_ = "sample",
  cluster_ = "cluster_id",
  max_rows = 500,
  max_cols = 100,
  fill_limits = NULL,
  clustering_col_min = -Inf,
  clustering_col_max = Inf,
  within_order_strategy = c("hclust", "sort")[2],
  dcast_fill = NA,
  return_data = FALSE,
  return_unassembled_plots = FALSE,
  rel_widths = c(1, 9),
  ...
)

Arguments

bw_data

a GRanges or data.table of bigwig signal. As returned from ssvFetchBam and ssvFetchBigwig

nclust

number of clusters

perform_clustering

should clustering be done? default is auto. auto considers if row_ has been ordered by being a factor and if cluster_ is a numeric.

row_

variable name mapped to row, likely id or gene name for ngs data. Default is "id" and works with ssvFetch* output.

column_

varaible mapped to column, likely bp position for ngs data. Default is "x" and works with ssvFetch* output.

fill_

numeric variable to map to fill. Default is "y" and works with ssvFetch* output.

facet_

variable name to facet horizontally by. Default is "sample" and works with ssvFetch* output. Set to "" if data is not facetted.

cluster_

variable name to use for cluster info. Default is "cluster_id".

max_rows

for speed rows are sampled to 500 by default, use Inf to plot full data

max_cols

for speed columns are sampled to 100 by default, use Inf to plot full data

fill_limits

limits for fill legend. values will be cropped to this range if set. Default of NULL uses natural range of fill_.

clustering_col_min

numeric minimum for col range considered when clustering, default in -Inf

clustering_col_max

numeric maximum for col range considered when clustering, default in Inf

within_order_strategy

one of "hclust" or "sort". if hclust, hierarchical clustering will be used. if sort, a simple decreasing sort of rosSums.

dcast_fill

value to supply to dcast fill argument. default is NA.

return_data

logical. If TRUE, return value is no longer ggplot and is instead the data used to generate that plot. Default is FALSE.

return_unassembled_plots

logical. If TRUE, return list of heatmap and cluster-bar ggplots. Can be customized and passed to assemble_heatmap_cluster_bars

rel_widths

numeric of length 2. Passed to cowplot::plot_grid. Default is c(1, 9).

...

addtional arguments passed to cowplot::plot_grid

Value

ggplot heatmap of signal profiles, facetted by sample

Examples

#the simplest use
ssvSignalHeatmap.ClusterBars(CTCF_in_10a_profiles_gr)
ssvSignalHeatmap.ClusterBars(CTCF_in_10a_profiles_gr, rel_widths = c(1, 5))

#clustering can be done manually beforehand
clust_dt = ssvSignalClustering(CTCF_in_10a_profiles_gr, nclust = 3)
ssvSignalHeatmap.ClusterBars(clust_dt)

[Package seqsetvis version 1.12.0 Index]