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Volcano plot of DE results

Source: R/plot_volcano.R
plot_volcano.Rd

This function creates a volcano plot to visualize the results of differential expression (DE) analysis performed by DE_between_group() or DE_between_time(). The plot displays log2 fold change on the x-axis and -log10 adjusted p-value on the y-axis, with DE features highlighted based on specified thresholds. If no thresholds are provided, the function will use the thresholds that were applied when running DE_between_group() or DE_between_time().

Usage

plot_volcano(
  DE_out,
  group1,
  group2,
  time,
  group,
  time1,
  time2,
  logFC_thres = NULL,
  adjP_thres = NULL,
  label = FALSE,
  fontsize = 8,
  ...
)

Arguments

DE_out

Output from DE_between_group() or DE_between_time()

group1

(Required for DE_between_group() output) Name of the first group for comparison

group2

(Required for DE_between_group() output) Name of the second group for comparison

time

(Required for DE_between_group() output) Time point for comparison

group

(Required for DE_between_time() output) Name of the group for comparison

time1

(Required for DE_between_time() output) First time point for comparison

time2

(Required for DE_between_time() output) Second time point for comparison

logFC_thres

(Optional) Log2 fold change threshold for highlighting DE features, default is NULL (using threshold when DE_between_group() or DE_between_time() was run)

adjP_thres

(Optional) Adjusted p-value threshold for highlighting DE features, default is NULL (using threshold when DE_between_group() or DE_between_time() was run)

label

(Optional) Whether to label names of DE features on the plot (default is FALSE)

fontsize

(Optional) Font size for the plot (default is 8)

...

Additional arguments for ggrepel::geom_text_repel() when label = TRUE

Value

A volcano plot of DE results

Examples

data("example")
example_obj <- normalise_to_start(example_obj)

DE_between_group_out <- DE_between_group(example_obj, assay = 2)
#> Non-NA replicate number filter not specified. Using minimum number of replicates across all groups and time points: 0
#> Comparing group IFNgamma to IFNbeta at Time 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma to IFNbeta at Time 2: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma to IFNbeta at Time 4: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma to IFNbeta at Time 6: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma to IFNbeta at Time 8: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma to IFNbeta at Time 24: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS to IFNbeta at Time 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS to IFNbeta at Time 2: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS to IFNbeta at Time 4: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS to IFNbeta at Time 6: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS to IFNbeta at Time 8: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS to IFNbeta at Time 24: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group untreated to IFNbeta at Time 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group untreated to IFNbeta at Time 8: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group untreated to IFNbeta at Time 24: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta to IFNgamma at Time 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta to IFNgamma at Time 2: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta to IFNgamma at Time 4: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta to IFNgamma at Time 6: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta to IFNgamma at Time 8: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta to IFNgamma at Time 24: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS to IFNgamma at Time 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS to IFNgamma at Time 2: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS to IFNgamma at Time 4: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS to IFNgamma at Time 6: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS to IFNgamma at Time 8: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS to IFNgamma at Time 24: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group untreated to IFNgamma at Time 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group untreated to IFNgamma at Time 8: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group untreated to IFNgamma at Time 24: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta to LPS at Time 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta to LPS at Time 2: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta to LPS at Time 4: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta to LPS at Time 6: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta to LPS at Time 8: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta to LPS at Time 24: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma to LPS at Time 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma to LPS at Time 2: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma to LPS at Time 4: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma to LPS at Time 6: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma to LPS at Time 8: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma to LPS at Time 24: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group untreated to LPS at Time 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group untreated to LPS at Time 8: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group untreated to LPS at Time 24: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta to untreated at Time 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta to untreated at Time 8: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta to untreated at Time 24: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma to untreated at Time 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma to untreated at Time 8: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma to untreated at Time 24: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS to untreated at Time 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS to untreated at Time 8: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS to untreated at Time 24: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero




plot_volcano(DE_between_group_out, group1 = "untreated", 
    group2 = "IFNbeta", time = 24,
    logFC_thres = 0.5, adjP_thres = 0.05, label = TRUE)