plot_violins | R Documentation |
Plot sample/feature violins
plot_violins(
object,
assay = assayNames(object)[1],
x,
fill,
color = NULL,
group = NULL,
facet = NULL,
nrow = NULL,
ncol = NULL,
dir = "h",
scales = "free",
labeller = label_value,
highlight = NULL,
palette = NULL,
fixed = list(na.rm = TRUE)
)
plot_feature_violins(
object,
assay = assayNames(object)[1],
x = "feature_id",
fill = "feature_id",
color = NULL,
n = 9,
facet = NULL,
nrow = NULL,
ncol = NULL,
dir = "h",
scales = "free",
labeller = label_value,
highlight = NULL,
fixed = list(na.rm = TRUE)
)
plot_sample_violins(
object,
assay = assayNames(object)[1],
x = "sample_id",
fill = if ("subgroup" %in% svars(object)) "subgroup" else "sample_id",
color = NULL,
n = 100,
facet = NULL,
nrow = NULL,
ncol = NULL,
dir = "h",
scales = "free",
labeller = label_value,
highlight = NULL,
fixed = list(na.rm = TRUE)
)
plot_subgroup_violins(
object,
assay = assayNames(object)[1],
subgroup,
x = "subgroup",
fill = "subgroup",
color = NULL,
highlight = NULL,
facet = "feature_id",
fixed = list(na.rm = TRUE)
)
object |
SummarizedExperiment |
assay |
string |
x |
svar (string) |
fill |
svar (string) |
color |
svar (string) |
group |
svar (string) |
facet |
svar (character vector) |
nrow |
NULL or number |
ncol |
NULL or number |
dir |
'h' or 'v' : are facets filled horizontally or vertically ? |
scales |
'free', 'free_x', 'free_y', or 'fixed' |
labeller |
label_both or label_value |
highlight |
fvar expressing which feature should be highlighted (string) |
palette |
named color vector (character vector) |
fixed |
fixed aesthetics |
n |
number |
subgroup |
subgroup svar |
ggplot object
plot_exprs
,
plot_densities
# data
file <- system.file('extdata/atkin.metabolon.xlsx', package = 'autonomics')
object <- read_metabolon(file)
object %<>% extract(, order(.$subgroup))
control_features <- c('biotin','phosphate')
fdata(object) %<>% cbind(control = .$feature_name %in% control_features)
# plot
plot_violins(object[1:12, ], x = 'feature_id', fill = 'feature_id')
plot_feature_violins(object[1:12, ])
plot_sample_violins(object[, 1:12], highlight = 'control')
plot_subgroup_violins(object[1:4, ], subgroup = 'subgroup')
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