This script allows you to perform different visualizations (bar, box, violin plots) using the results of the MetaProViz analysis

Bar, Box or Violin plot in Superplot style visualization

Usage

viz_superplot(
  data,
  metadata_sample = NULL,
  metadata_info = c(Conditions = "Conditions", Superplot = NULL),
  plot_type = "Box",
  plot_name = "",
  plot_conditions = NULL,
  stat_comparison = NULL,
  pval = NULL,
  padj = NULL,
  xlab = NULL,
  ylab = NULL,
  theme = NULL,
  color_palette = NULL,
  color_palette_dot = NULL,
  save_plot = "svg",
  print_plot = TRUE,
  path = NULL
)

Arguments

data

SummarizedExperiment (se) file including assay and colData. If se file is provided, metadata_sample is extracted from the colData of the se object. metadata_feature, if available, are extracted from the rowData. Alternatively provide a DF with unique sample identifiers as row names and metabolite numerical values in columns with metabolite identifiers as column names. Use NA for metabolites that were not detected.

metadata_sample

Optional: Only required if you did not provide se file in parameter data. Provide DF which contains metadata information about the samples, which will be combined with your input data based on the unique sample identifiers used as rownames. Default = NULL

metadata_info

Named vector including at least information on the conditions column: c(Conditions="ColumnName_metadata_sample"). Additionally Superplots can be made by adding Superplot ="ColumnName_metadata_sample", which are usually biological replicates or patient IDs. Default = c(Conditions="Conditions", Superplot = NULL)

plot_type

String with the information of the Graph style. Available options are Bar. Box and Violin Default = Box

plot_name

Optional: String which is added to the output files of the plot.

plot_conditions

Vector with names of selected Conditions for the plot. Can also be used to order the Conditions in the way they should be displayed on the x-axis of the plot. Default = NULL

stat_comparison

List of numeric vectors containing Condition pairs to compare based on the order of the plot_conditions vector. Default = NULL

pval

Optional: String which contains an abbreviation of the selected test to calculate p.value. For one-vs-one comparisons choose t.test or wilcox.test , for one-vs-all or all-vs-all comparison choose aov (=anova) or kruskal.test Default = NULL

padj

Optional: String which contains an abbreviation of the selected p.adjusted test for p.value correction for multiple Hypothesis testing. Search: ?p.adjust for more methods:"BH", "fdr", "bonferroni", "holm", etc.Default = NULL

xlab

Optional: String to replace x-axis label in plot. Default = NULL

ylab

Optional: String to replace y-axis label in plot. Default = NULL

theme

Optional: Selection of theme for plot, e.g. theme_grey(). You can check for complete themes here: https://ggplot2.tidyverse.org/reference/ggtheme.html. Default = NULL

color_palette

Optional: Provide customized color_palette in vector format. Default = NULL

color_palette_dot

Optional: Provide customized color_palette in vector format. Default = NULL

save_plot

Optional: Select the file type of output plots. Options are svg, pdf, png or NULL. Default = svg

print_plot

Optional: TRUE or FALSE, if TRUE plots are saved as an overview of the results. Default = TRUE

path

Optional: Path to the folder the results should be saved at. Default = NULL

Value

List with two elements: Plot and Plot_Sized

Examples

data(intracell_raw_se)
# only plot the first 2 metabolites
Res <- viz_superplot(data = intracell_raw_se[1:2, , drop = FALSE])
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: Removed 10 rows containing non-finite outside the scale range
#> (`stat_bracket()`).

#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: Removed 10 rows containing non-finite outside the scale range
#> (`stat_bracket()`).


data(intracell_raw)
Intra <- intracell_raw[, c(1:6)] %>% tibble::column_to_rownames("Code")
Res <- viz_superplot(
    data = Intra[, -c(1:3)],
    metadata_sample = Intra[, c(1:3)]
)
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: Removed 10 rows containing non-finite outside the scale range
#> (`stat_bracket()`).

#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: Removed 10 rows containing non-finite outside the scale range
#> (`stat_bracket()`).