plot_gam: Plot gam model fit for multiple genes and archetypes...

In vitkl/ParetoTI: R toolbox for Archetypal Analysis and Pareto Task Inference on single cell data

Description

plot_gam() plots gam model fit for multiple features (genes) and archetypes

Usage

plot_gam(gam_deriv = NULL, gam_fit, data, feature = NULL,
  archetype = NULL, groupCovs = NULL, title_size = 10,
  point_size = 1, point_alpha = 0.1, point_position = c("identity",
  "jitter"), rug_size = 1, rug_alpha = 0.1,
  title = "GAM model: gene expression = function(distance from archetype)")

Arguments

gam_deriv	object with multiple gam fits (many arhetypes, many features). Either gam_deriv or gam_fit must be provided.
gam_fit	a fitted gam object as produced by gam().
data	data.table dim(examples, dimensions) that includes distance of each example to archetype in columns given by arc_col and feature values given by feature. Must be provided.
feature	character vector, which features (e.g. genes) to plot?
archetype	character vector, which archetypes to plot?
groupCovs	argument for plotGAM
title_size	size of individial plot titles and axis titles
point_position	point position option, a way to add jitter but "identity" by default
title	main title for all features and archetypes
point_size/rug_size/point_alpha/rug_alpha	size and alpha controls for points and geom_rug.

Details

Plotting of multiple gam fits is inspired by https://stackoverflow.com/questions/49471300/gam-plots-with-ggplot

Value

plot_gam() list (S3 object, plot_gam) containing data.table-s for each predictor in gam model

vitkl/ParetoTI documentation built on Feb. 11, 2020, 1:36 a.m.