plot heatmap from a module
plot_module_heatmap( compendium = "vespucci", module = NULL, normalization = "tpm", type = "json", plot = TRUE, alternativeColoring = TRUE, min = -6, max = 6, sorted = FALSE )
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 |
Either a json, an html, a plotly htmlwidget, or a list of sorted features
if (FALSE) { 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) }