plot_boxplots {autonomics} | R Documentation |
Plot sample/feature boxplots
plot_boxplots( object, x, fill, color = NULL, facet = NULL, highlight = NULL, fixed = list(na.rm = TRUE) ) plot_sample_boxplots( object, x = sample_id, fill = sample_id, color = NULL, highlight = NULL, fixed = list(na.rm = TRUE) ) plot_feature_boxplots( object, x = feature_id, fill = feature_id, color = NULL, highlight = NULL, fixed = list(na.rm = TRUE) ) plot_subgroup_boxplots( object, subgroup, x = !!enquo(subgroup), fill = !!enquo(subgroup), color = NULL, highlight = NULL, facet = feature_id, fixed = list(na.rm = TRUE) )
object |
SummarizedExperiment |
x |
svar mapped to x |
fill |
svar mapped to fill |
color |
svar mapped to color |
facet |
svar mapped to facet |
highlight |
fvar expressing which feature should be highlighted |
fixed |
fixed aesthetics |
subgroup |
subgroup svar symbol |
ggplot object
plot_sample_densities
,
plot_sample_violins
# data require(magrittr) file <- download_data('halama18.metabolon.xlsx') object <- read_metabolon(file, plot = FALSE) object %<>% extract(, order(.$Group)) fdata(object) %<>% cbind( control=.$feature_name %in% c('biotin','phosphate')) # plot plot_boxplots(object[1:9,], x = feature_id, fill = feature_id) plot_boxplots(object[,1:9], x = sample_id, fill = sample_id ) plot_feature_boxplots(object[1:9, ]) plot_sample_boxplots(object[, 1:12]) plot_sample_boxplots(object[, 1:12], highlight = control) plot_subgroup_boxplots(object[1:2, ], subgroup = Group)