plot_subChar_multiGroup

Source: R/plot_subChar_multiGroup.R

This function is for plotting the results of subgroup lipid characteristics differential expression analysis.

plot_subChar_multiGroup(subChar_se, subChar_feature)

Arguments

subChar_se

A SummarizedExperiment object with results computed by subChar_multiGroup.

subChar_feature

Character. A feature selected by users from subChar to visualize the specific plot for the selected category of that characteristic. For example, if subChar is 'class' and subChar_feature is 'Cer', the resulting plots will display data for 'Cer' within the 'class' category.

Value

Return a list with 5 static plots, 4 interactive plots, and 5 data frames.

  1. static_barPlot: a static bar plot shows the average expression of each sample group and highlights significant differences between groups based on a user-selected characteristic.

  2. static_barPlot_sqrt: a static bar plot shows the average expression of each sample group and highlights significant differences between groups based on a user-selected characteristic. NOTE: the y axis is sqrt-scaled.

  3. static_linePlot: a static line plot shows the average expression of each sample group and highlights significant differences between the groups based on a user-selected characteristic.

  4. static_linePlot_sqrt: a static line plot shows the average expression of each sample group and highlights significant differences between the groups based on a user-selected characteristic. NOTE: the y axis is sqrt-scaled.

  5. static_boxPlot: a static box plot of ctrl group and experiment group.

  6. interactive_barPlot: an interactive bar plot shows the average expression of each sample group and highlights significant differences between groups based on a user-selected characteristic.

  7. interactive_barPlot_sqrt: an interactive bar plot shows the average expression of each sample group and highlights significant differences between groups based on a user-selected characteristic. NOTE: the y axis is sqrt-scaled.

  8. interactive_linePlot: an interactive line plot shows the average expression of each sample group and highlights significant differences between the groups based on a user-selected characteristic.

  9. interactive_linePlot_sqrt: an interactive line plot shows the average expression of each sample group and highlights significant differences between the groups based on a user-selected characteristic. NOTE: the y axis is sqrt-scaled.

  10. table_barPlot: table for plotting bar plots

  11. table_linePlot: table for plotting line plots

  12. table_boxPlot: table for plotting box plots

  13. table_char_index: table with the value calculated by the weighted average of lipid characteristics abundance

  14. table_index_stat: table with statistics of control and experiment groups

Examples

data("se_multiGroup")
processed_se <- data_process(
    se=se_multiGroup, exclude_missing=TRUE, exclude_missing_pct=70,
    replace_na_method='min', replace_na_method_ref=0.5,
    normalization='Percentage')
subChar_se <- subChar_multiGroup(
    processed_se, char='Total.C', subChar='class', ref_group='ctrl',
    post_hoc='One-way ANOVA', post_hoc_sig='pval', post_hoc_p_cutoff=0.05,
    transform='log10')
#> Warning: longer object length is not a multiple of shorter object length
#> There are 4 ratio characteristics that can be converted in your dataset.
subChar_plot <- plot_subChar_multiGroup(subChar_se, subChar_feature='CL')