Function reference • jamma

Jamma package About the jamma package
`jamma`	jamma: MA-plots for omics data
Plot functions Functions that assist with R plotting
`ggjammaplot()` `jammaplot()`	Produce MA-plot of omics data.
`volcano_plot()`	Volcano plot
Matrix functions Functions that manipulate numeric matrix data
`centerGeneData()`	Center gene data
`jammacalc()`	Calculate MA-plot data
`jammanorm()`	Normalize data using MA-plot logic
`matrix_to_column_rank()`	Convert numeric matrix to column-rank data
Utility functions Functions that are used internally by jamma functions
`blockArrowMargin()`	Draw block arrows in plot margins
`find_colname()`	Find colname by string or pattern
`fold_to_log2fold()`	Convert normal signed fold change to log2 fold change
`get_se_assaydata()`	Get SummarizedExperiment assay matrix data
`gradient_rect()`	Rectangle with color gradient fill
`handle_highlightPoints()`	Handle highlightPoints argument to jammaplot()
`log2fold_to_fold()`	Convert log2 fold change to signed fold change
`logAxis()`	Log-scaled axis including transformed P-values
`outer_legend()`	Add legend in the outer margin
`points2polygonHull()`	define a polygon hull around points
`update_function_params()`	Update function default parameters
`update_list_elements()`	Update a subset of list elements (deprecated)
ggtext functions Functions that are dependent upon the ggtext package
`element_grob.element_textbox_colorsub()`	Custom ggplot2 element textbox highlight grob
`element_textbox_colorsub()`	Custom ggplot2 element textbox highlight
Deprecated functions Functions that will be removed in a future release
`centerGeneData_v1()`	Center gene data

Reference

Jamma package

Plot functions

Matrix functions

Utility functions

ggtext functions

Deprecated functions