plot_module_heatmap: plot heatmap from a module

In onertipaday/rcompass: R Client for the COMPASS GrapgQL API

Description

plot heatmap from a module

Usage

plot_module_heatmap(
  compendium = "vespucci",
  module = NULL,
  normalization = "tpm",
  type = "json",
  plot = TRUE,
  alternativeColoring = TRUE,
  min = -6,
  max = 6,
  sorted = FALSE
)

Arguments

compendium	A string - the selected compendium
module	A matrix with valid rownames (biofeatureNames) and colnames (samplesetsNames)
normalization	A string - either 'limma','tpm' or legacy as normalization
type	A string - either 'html' or 'json
plot	A logical - it returns the graphics object
alternativeColoring	A logical - if TRUE (defautl) a color blind friendly palette is used
min	A numeric (-6 default)
max	A numeric (6 default)
sorted	A logical - it returns sorted index for both bf and ss

Value

Either a json, an html, a plotly htmlwidget, or a list of sorted features

Examples

## Not run: 
gene_names <- get_biofeature_id(id_In = c('VIT_00s0246g00220',
'VIT_00s0332g00060','VIT_00s0332g00110'), useIds = F)
mod <- create_module(biofeaturesNames=gene_names$id, normalization = "tpm", useIds = T)
plot_module_heatmap(module = mod, normalization = "tpm", plot = TRUE)
sorted_idx <- plot_module_heatmap(mod = mod, sorted = TRUE, plot = FALSE)

## End(Not run)

onertipaday/rcompass documentation built on Sept. 18, 2021, 5:13 p.m.