plot_subChar_twoGroup

Source: R/subChar_twoGroup.R

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

plot_subChar_twoGroup(subChar_se, subChar_feature)

Arguments

subChar_se

A SummarizedExperiment object with results computed by subChar_twoGroup.

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, 5 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 two 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 two 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 two 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 two 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 two 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 two 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 two 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 two groups based on a user-selected characteristic. NOTE: the y axis is sqrt-scaled.

  10. interactive_boxPlot: an interactive box plot of ctrl group and experiment group.

  11. table_barPlot: table for plotting bar plots

  12. table_linePlot: table for plotting line plots

  13. table_boxPlot: table for plotting box plots

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

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

Examples

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')
subChar_se <- subChar_twoGroup(processed_se, char="Total.C", subChar="class",
    ref_group="ctrl", test='t-test', significant="pval", p_cutoff=0.05,
    FC_cutoff=1, transform='log10')
#> There are 4 ratio characteristics that can be converted in your dataset.
subChar_feature_list <- unique(
    extract_summarized_experiment(subChar_se)$all_deChar_result$sub_feature)
res_plot <- plot_subChar_twoGroup(subChar_se, subChar_feature="Cer")