plotConfidenceIntervals: plotConfidenceIntervals

In genesofeve/ProjectR: Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering

plotConfidenceIntervals

Description

Generate point and line confidence intervals from provided estimates.

Usage

plotConfidenceIntervals(
  confidence_intervals,
  interval_name = c("low", "high"),
  pattern_name = NULL,
  sort = TRUE,
  genes = NULL,
  weights = NULL,
  weights_clip = 0.99,
  weights_vis_norm = "none",
  weighted = FALSE
)

Arguments

confidence_intervals	A dataframe of features x estimates.
interval_name	Estimate column names. Default: c("low","high")
pattern_name	string to use as the title for plots.
sort	Boolean. Sort genes by their estimates (default = TRUE)
genes	a vector with names of genes to include in plot. If sort=F, estimates will be plotted in this order.
weights	optional. weights of features to include as annotation.
weights_clip	optional. quantile of data to clip color scale for improved visualization. Default: 0.99
weights_vis_norm	Which version of weights to visualize as a heatmap. Options are "none" (uses provided weights) or "quantiles". Default: none
weighted	specifies whether the confidence intervals in use are weighted by the pattern and labels plots accordingly

Value

A list with pointrange estimates and a heatmap of pattern weights.

genesofeve/ProjectR documentation built on Nov. 16, 2024, 8:20 p.m.