ctPlotPointsAnnotation: ctPlotPointsAnnotation

In jrboyd/seqtsne: Application of t-sne to NGS Genomic Signal Profiles

ctPlotPointsAnnotation

Description

ctPlotPointsAnnotation

Usage

ctPlotPointsAnnotation(
  sts,
  meta_data = NULL,
  feature_name = NULL,
  signal_name = NULL,
  anno_var = NULL,
  anno_var_label = anno_var,
  bg_color = "gray60",
  return_data = FALSE,
  point_size = 1
)

Arguments

sts	A ChIPtSNE object with ssvQC.prepSignal already called.
meta_data	A data.frame containing "id" and anno_var. Will use cluster assignment if not set.
feature_name	Feature name present in sts. With default of NULL, first feature name will be used.
signal_name	Signal name present in sts. With default of NULL, first signal name will be used.
anno_var	Variable to extract from meta_data for plotting.
anno_var_label	Label to use for color legend. Default is anno_var.
bg_color	Color to use for plot background. Default is "gray60".
return_data

Value

ggplot with color of t-SNE points determined by annotation in meta_data.

Examples

data(ex_sts)
ctPlotPointsAnnotation(sts)

#example using peak call
query_gr = sts$features_config$assessment_features[[1]]
meta_data = data.table(id = names(query_gr), chromosome = as.character(seqnames(query_gr)))
ctPlotPointsAnnotation(sts, meta_data = meta_data, anno_var = "chromosome")

jrboyd/seqtsne documentation built on Nov. 5, 2022, 6:37 a.m.