Package index • NGCHMR

Creating and Saving an NG-CHM

chmNew(): Create a new NGCHM.

chmExportToHTML(): Export a standalone HTML containing the NGCHM to a file.

chmExportToFile(): Export a standalone NGCHM to a file.

Covariate Bars

chmNewCovariate(): Create a new Covariate for adding to an NGCHM auxilary dataset.

chmAddCovariateBar(): Add a covariate bar to a NGCHM.

chmAddCovariate(): Add a covariate to an auxiliary dataset.

chmNewCovariateBar(): Create a new covariate Bar for a NGCHM

chmCovariate(): Get a covariate attached to an NG-CHM dataset.

chmCovariateBar(): Get a covariate bar attached to an NG-CHM.

Colors and Color Maps

chmNewColorMap(): Create a new Color Map for use in constructing a NGCHM

chmAddColormap(): Add a colormap to a NGCHM.

`chmColorMap<-`(): Set the color map of an NG-CHM object

chmColorMap(): Get the color map of an NG-CHM object.

chmColors(): Get the colors of an ngchmColormap, ngchmLayer, ngchmBar, or ngchmCovariate.

`chmColors<-`(): Set the colors of an ngchmColormap, ngchmLayer, ngchmBar, or ngchmCovariate.

chmAdd(): Add a list of objects to a NGCHM.

Data Layers

chmNewDataLayer(): Create a new Data Layer for a NGCHM.

chmAddLayer(): Add a Layer to a NGCHM.

chmLayer(): Get a specified Data Layer from an NG-CHM.

chmAdd(): Add a list of objects to a NGCHM.

Specifying Axis Type

For automatically adding linkouts

chmAddAxisType(): Add an axis type to a NGCHM.

Add Scatter Plot Coordinates

chmAddPCA(): Add PCA coordinates to an NG-CHM.

chmAddUMAP(): Add UMAP coordinates to an NG-CHM.

chmAddUWOT(): Add UWOT::UMAP coordinates to an NG-CHM.

chmAddTSNE(): Add TSNE coordinates to an NG-CHM.

chmAddReducedDim(): Add reduced dimension coordinates to an NG-CHM.

Row and Column Ordering and Dendrograms

`chmColOrder<-`(): Set the column order of data shown in a NGCHM.

`chmRowOrder<-`(): Set the row order of data shown in a NGCHM.

Map Properties

chmHasProperty(): Determine if the NG-CHM has the given property.

chmGetProperty(): Get Property from NG-CHM

chmNewProperty(): Create a new Property for adding to a NGCHM.

chmAddProperty(): Add custom property to a NGCHM.

chmProperty(): Get the value of an NG-CHM property.

`chmProperty<-`(): Set the value of an NG-CHM property.

chmAdd(): Add a list of objects to a NGCHM.

Adding Gaps

chmTreeGaps(): Creates new treeCuts object