Volcano trelliscope building function for fold_change — trelli_foldchange

Specify a plot design and cognostics for the fold_change volcano trelliscope. Fold change must be grouped by an emeta column, which means both an omicsData object and statRes are required to make this plot.

trelli_foldchange_volcano(
  trelliData,
  comparison = "all",
  cognostics = "biomolecule count",
  p_value_thresh = 0.05,
  ggplot_params = NULL,
  interactive = FALSE,
  path = .getDownloadsFolder(),
  name = "Trelliscope",
  test_mode = FALSE,
  test_example = 1,
  single_plot = FALSE,
  ...
)

Arguments

trelliData: A trelliscope data object with omicsData and statRes results. Required.
comparison: The specific comparison to visualize in the fold_change volcano. See attr(statRes, "comparisons") for the available options. If all comparisons are desired, the word "all" can be used, which is the default. Required.
cognostics: A vector of cognostic options for each plot. Valid entries are "biomolecule count", "proportion significant", "proportion significant up", and "proportion significant down". Default is "biomolecule count".
p_value_thresh: A value between 0 and 1 to indicate significant biomolecules for p_value_test. Default is 0.05.
ggplot_params: An optional vector of strings of ggplot parameters to the backend ggplot function. For example, c("ylab(”)", "xlab(”)"). Default is NULL.
interactive: A logical argument indicating whether the plots should be interactive or not. Interactive plots are ggplots piped to ggplotly (for now). Default is FALSE.
path: The base directory of the trelliscope application. Default is Downloads.
name: The name of the display. Default is Trelliscope.
test_mode: A logical to return a smaller trelliscope to confirm plot and design. Default is FALSE.
test_example: A vector of plot indices to return for test_mode. Default is 1.
single_plot: A TRUE/FALSE to indicate whether 1 plot (not a trelliscope) should be returned. Default is FALSE.
...: Additional arguments to be passed on to the trelli builder

Value

No return value, builds a trelliscope display of fold-change volcano plots that is stored in `path`

Author

David Degnan, Lisa Bramer

Examples

# \donttest{
if (interactive()) {
library(pmartRdata)

# Transform the data
omicsData <- edata_transform(omicsData = pep_object, data_scale = "log2")

# Group the data by condition
omicsData <- group_designation(omicsData = omicsData, main_effects = c("Phenotype"))

# Apply the IMD ANOVA filter
imdanova_Filt <- imdanova_filter(omicsData = omicsData)
omicsData <- applyFilt(filter_object = imdanova_Filt, omicsData = omicsData,
                       min_nonmiss_anova = 2)

# Normalize my pepData
omicsData <- normalize_global(omicsData, "subset_fn" = "all", "norm_fn" = "median",
                             "apply_norm" = TRUE, "backtransform" = TRUE)

# Implement the IMD ANOVA method and compute all pairwise comparisons 
# (i.e. leave the `comparisons` argument NULL)
statRes <- imd_anova(omicsData = omicsData, test_method = 'combined')

# Generate the trelliData object
trelliData4 <- as.trelliData(omicsData = omicsData, statRes = statRes)
## Build fold_change bar plot with statRes data grouped by edata_colname.
trelli_panel_by(trelliData = trelliData4, panel = "RazorProtein") %>% 
  trelli_foldchange_volcano(comparison = "all", test_mode = TRUE, test_example = 1:10,
                            cognostics = c("biomolecule count", "proportion significant"),
                            path = tempdir())

DONTSHOW({closeAllConnections()})
}
# }