Displays a correlation matrix of the quantitative data of a numeric matrix.

This function is a wrapper to heatmap.2() that displays assay data in an instance of SummarizedExperiment. For more details, see heatmap.2().

omXplore_heatmap_ui(id)

omXplore_heatmap_server(
  id,
  obj = reactive({
     NULL
 }),
  i = reactive({
     NULL
 })
)

omXplore_heatmap(obj, i)

heatmapD(
  qdata,
  conds,
  distance = "euclidean",
  cluster = "complete",
  dendro = FALSE
)

mv.heatmap(
  x,
  col = grDevices::heat.colors(100),
  srtCol = NULL,
  labCol = NULL,
  labRow = NULL,
  key = TRUE,
  key.title = NULL,
  main = NULL,
  ylab = NULL
)

heatmapForMissingValues(
  x,
  col = NULL,
  srtCol = NULL,
  labCol = NULL,
  labRow = NULL,
  key = TRUE,
  key.title = NULL,
  main = NULL,
  ylab = NULL
)

Arguments

id: A character(1) which is the id of the shiny module.
obj: An instance of a class MultiAssayExperiment.
i: An integer which is the index of the assay in the param obj
qdata: A data.frame() of quantitative data.
conds: A vector indicating the name of each sample.
distance: The distance used by the clustering algorithm to compute the dendrogram.
cluster: the clustering algorithm used to build the dendrogram.
dendro: A boolean to indicate fi the dendrogram has to be displayed
x: A matrix or array containing the quantitative data.
col: Colors used for the image. Defaults to heat colors (heat.colors).
srtCol: Angle of column conds, in degrees from horizontal
labCol: Character vectors with column conds to use.
labRow: Character vectors with row conds to use.
key: Logical indicating whether a color-key should be shown.
key.title: Main title of the color key. If set to NA no title will be plotted.
main: Main title; default to none.
ylab: y-axis title; default to none.

Value

A shiny app

A heatmap

Author

Florence Combes, Samuel Wieczorek, Enora Fremy

Examples

if (FALSE) { # \dontrun{
  data(vdata)
  omXplore_heatmap(vdata, 1)
} # }