update_annotations.genes: Update Gene Annotations

In axm323/dataVisEasy: datavisEasy: Data visualizations Using Annotations Made Easy

Update Gene Annotations

Description

Update gene annotations stored in annotations.genes parameter of the params list object. See set_annotations.genes for intially setting the annotations.

Usage

update_annotations.genes(annotation, values)

Arguments

annotation	title of annotation to be updated or added. If already found in the colnames of the annotations.genes data frame, the previous values for that column will be replaced with the supplied values here. If not found in the colnames of the annotations.genes data frame, values will be added as a new annotation column under the name indicated.
values	data frame of values corresponding to the annotation to be updated or added (gene names should be in rownames).

Details

If the name of the supplied annotation already exists, will overwrite the previous values. Number of values in updated annotation do not need to be the same length as the pre-existing annotations. This function will merge the annotations, see full_join. Any missing values will be set to "No_Annot" signifying that no annotation was provided. This is especially useful if annotating clusters where the genes being clustered and annotated is a subset of all genes present, see extractClusters if added annotations are identifications of cluster groups. If new or updated values should be shown in the heatmap, must rerun set_annot_genes. To add specific colors for the new annotations, see set_annot_cols and update_annot_cols.

Author(s)

~~Alison Moss~~

See Also

See set_annotations.genes for how to set initially Works the same as for sample annotations, see update_annotations for examples

axm323/dataVisEasy documentation built on Feb. 1, 2024, 11:53 p.m.