DE number between groups

Plot the number of differentially expressed features between groups over time, using the output of DE_between_group().

DE features were pre-filtered with DE_between_group(), but by specifying adjP_thres and logFC_thres, users can re-filter the DE features for plotting.

Usage

plot_DE_between_group(
  DE_between_group_out,
  group = NULL,
  fontsize = 8,
  adjP_thres = NULL,
  logFC_thres = NULL
)

Arguments

DE_between_group_out

Output of DE_between_group(), a list with all_list, de_list, ref_groups, all_groups elements.

group

A character vector specifying which groups to use as the reference (Cond1) for plotting. If NULL, all groups in the output will be plotted. (default is NULL)

fontsize

Font size for the plot (default is 8)

adjP_thres

(Optional) Threshold for adjusted p-value to consider a feature as differentially expressed, for re-filtering the DE features. (default is NULL, no re-filtering)

logFC_thres

(Optional) Threshold for log2 fold change to consider a feature as differentially expressed, for re-filtering the DE features. (default is NULL, no re-filtering)

Value

A series of line plots showing the number of DE features over time for each group comparison.

Examples

data(example_obj)
example_obj <- normalise_to_start(example_obj)
#> Normalising to group baseline at each feature's first non-NA time point.

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 untreated vs IFNbeta: time points only in IFNbeta: 2, 4, 6; only in untreated: none
#> 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 untreated vs IFNgamma: time points only in IFNgamma: 2, 4, 6; only in untreated: none
#> 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 untreated vs LPS: time points only in LPS: 2, 4, 6; only in untreated: none
#> 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 IFNbeta vs untreated: time points only in untreated: none; only in IFNbeta: 2, 4, 6
#> 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 IFNgamma vs untreated: time points only in untreated: none; only in IFNgamma: 2, 4, 6
#> 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 LPS vs untreated: time points only in untreated: none; only in LPS: 2, 4, 6
#> 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_DE_between_group(DE_between_group_out, fontsize = 8)
#> $IFNbeta

#> 
#> $IFNgamma

#> 
#> $LPS

#> 
#> $untreated

#>