parameters: List Object Holding Parameters Called by Other Functions

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

List Object Holding Parameters Called by Other Functions

Description

The functions in the dataVisEasy package often call upon variables stored within this list object for annotations, coloring, and to keep consistent throughout the use of the package without having to unnecessarily spec

Format

The format is a list of 9 items:

scale.range

the scale of heatmaps, default set to c(-1,1), see set_scale.range

scale.colors

default colors for heatmaps, default set to c("blue","black","yellow"), see set_scale.colors

n.colors.range

number of distinct colors in a heatmap, default set to 100, see set_n.colors.range

annotations

Will hold a dataframe of annotations for samples (data columns), see set_annotations. Initialized as NA.

annot_samps

Will hold a dataframe of annotations to be displayed as tracks along heatmaps, see set_annot_samps. Initialized as NA.

annotations.genes

Will hold a dataframe of annotations for genes (data rows), see set_annotations.genes. Initialized as NA.

annot_genes

Will hold a dataframe of gene annotations to be displayed as tracks along heatmaps, see set_annot_genes. Initialized as NA.

annot_cols

Specific colors to accompany annotations, will hold a list of color assignments, see set_annot_cols. Initialized as NA.

expression_gradiet.colors

color range for plots colored by expression level, default set to c("blue","lightblue","gray","indianred","firebrick"), see set_expression_gradient.colors

Details

All of the parameters stored in params can be set and updated using the functions listed below. Likewise, all of these objects can be accessed from the terminal using params$'parameter' where 'parameter' represents any of the list object the user may wish to check on or change.

The functions in the dataVisEasy package often call upon variables stored within this list object for annotations, coloring, and to keep consistent throughout the use of the package without having to unnecessarily specify various parameters in the functions themselves. For example, in the case of heatmaps, instead of having to specify the colors or the range of the heatmap within the function every time it is used, the functions themselves simply refer to variables stored within this list object. Similarly, once annotations for the data in question are set and stored here, all functions in the package will refer directly to that stored object, allowing for ease of use and consistency across all included functions. While on the front end this may take more time to set up the annotations and variables properly, once they are set the user need not worry about keeping track of our specifying these parameters later on. Likewise, these variables can be changed or updated at any time. For example if the user wishes to change the scale range of the heatmap, they need to set it using set_scale.range. The new values they have set will then be used until it is changed to something else.

See Also

See set_scale.range, set_scale.colors, set_n.colors.range, set_annotations, set_annot_samps, set_annotations.genes, set_annot_genes, set_annot_cols, and set_expression_gradient.colors for information on changing and setting these parameters

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