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