ssvSignalHeatmap.ClusterBars {seqsetvis} | R Documentation |
Compared to ssvSignalHeatmap, cluster_bars are displayed on the left once instead of for each facet
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), ... )
bw_data |
a GRanges or data.table of bigwig signal.
As returned from |
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 |
rel_widths |
numeric of length 2. Passed to cowplot::plot_grid. Default is c(1, 9). |
... |
addtional arguments passed to cowplot::plot_grid |
ggplot heatmap of signal profiles, facetted by sample
#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)