This function shows the significant lipid species based on different lipid characteristics and visualizes the difference between control and experimental groups.
char_association(deSp_se, char)The resulting SummarizedExperiment object from the differential
expression analysis function, such as deSp_twoGroup and
deSp_multiGroup.
Character. A lipid characteristic selected from the common list
returned by list_lipid_char.
Return a list with 3 tables, 3 interactive plots, and 3 static plots.
interactive_barPlot & static_barPlot: a bar plot distinguishes significant groups (values) exhibiting a mean fold change greater than 1. (NOTE: The bar chart is not generate for multiple-group data.)
interacitve_lollipop & static_lollipop: a lollipop plot compares all significant groups within the selected characteristic by log2(fold change) for two-group data and -log10(p-value) for multiple-group data.
interactive_wordCloud & static_wordCloud: a word cloud visualizes the frequency of each group (value) associated with the chosen characteristic.
table_barPlot: table for plotting bar plots.
table_lollipop: table for plotting lollipop plots.
table_wordCloud: table for plotting word cloud.
data("de_data_twoGroup")
processed_se <- data_process(
de_data_twoGroup, exclude_missing=TRUE, exclude_missing_pct=70,
replace_na_method='min', replace_na_method_ref=0.5,
normalization='Percentage')
deSp_se <- deSp_twoGroup(processed_se, ref_group='ctrl', test='t-test',
significant='pval', p_cutoff=0.05, FC_cutoff=1, transform='log10')
result <- char_association(deSp_se, char='class')