Prepare ALE data for violin plots
ale2violin( iMatrixAle = NULL, iMatrixAleGrp = NULL, groups, facet_groups = groups, facet_name = "Group", maxGroupMeanALE = 2, removeAboveAleNum = "ale3", maxGroupMeanFloor = 0, returnAll = FALSE, geneLists, lineAlpha = 0.1, subsetFunc = NULL, make_ggplots = TRUE, verbose = FALSE, ... )
groups | vector of group labels, named by |
---|---|
facet_groups | vector of group labels, named by |
facet_name | character string used to label the |
maxGroupMeanALE | numeric value indicating the threshold for including an ALE in the output data, where the max group mean (the highest group mean) is at least this value. |
removeAboveAleNum | character string of the ALE colname to remove, restricting data to include only ALE values below this number. For example "ale3" would remove "ale3" and all higher ALE numbers, thereby restricting data to "ale1" and "ale2". |
maxGroupMeanFloor | numeric threshold used as a noise floor. |
returnAll | logical indicating whether to return intermediate data formats in the output results list. |
geneLists | list containing vectors of genes, or a data.frame with two columns "gene_name" and "geneList", used to assign genes to one or more lists in the resulting violin plot. |
lineAlpha | numeric value of alpha transparency, scaled between 0 and 1, used to draw lines from "_ale1" to "_ale2" on the violin plot. |
subsetFunc | optional function that takes the tall format data used in the
primary violin plot, and returns data in the same format after
applying logic specific for filtering this data. Intended to
restrict display of genes to |
make_ggplots | logical indicating whether to create plot objects using ggplot2. |
verbose | logical indicating whether to print verbose output |
... | additional arguments are ignored. |
iMatrixALE | numeric matrix of expression data containing
ALE rows, as output from |
This function takes output from tx2ale()
, applies some filtering
to the output data, then returns a tall data.frame sufficient
for viewing as a violin plot using ggplot2::geom_violin()
.
Other jam ALE-specific RNA-seq functions:
getFirstStrandedFromGRL()
,
tx2ale()