DE number between time points

Plot the number of differentially expressed features between time points within each group with heatmaps

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

Usage

plot_DE_between_time(
  DE_between_time_out,
  value = TRUE,
  fontsize = 8,
  nrow = 1,
  heatmap_width = 4,
  heatmap_unit = "cm",
  adjP_thres = NULL,
  logFC_thres = NULL
)

Arguments

DE_between_time_out

Output of DE_between_time(), a list with all_list, de_list, time_series elements.

value

Whether to display the actual number of DE features in each heatmap cell (default is TRUE)

fontsize

Font size for the heatmap displaying the number of DE features between time points (default is 8)

nrow

Number of rows for arranging the heatmaps (default is 1)

heatmap_width

Width of each heatmap (default is 4)

heatmap_unit

Unit for the heatmap width (default is "cm")

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

One heatmap per group showing the number of DE features between time points for each group, with the same scale across groups for easy comparison. The heatmap cells are optionally annotated with the number of DE features.

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_time_out <- DE_between_time(example_obj, assay = 1)
#> Non-NA replicate number filter not specified. Using minimum number of replicates across all groups and time points: 0
#> Comparing group IFNbeta time 2 to 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta time 4 to 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta time 6 to 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta time 8 to 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta time 24 to 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta time 4 to 2: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta time 6 to 2: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta time 8 to 2: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta time 24 to 2: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta time 6 to 4: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta time 8 to 4: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta time 24 to 4: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta time 8 to 6: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta time 24 to 6: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNbeta time 24 to 8: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma time 2 to 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma time 4 to 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma time 6 to 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma time 8 to 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma time 24 to 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma time 4 to 2: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma time 6 to 2: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma time 8 to 2: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma time 24 to 2: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma time 6 to 4: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma time 8 to 4: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma time 24 to 4: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma time 8 to 6: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma time 24 to 6: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group IFNgamma time 24 to 8: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS time 2 to 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS time 4 to 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS time 6 to 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS time 8 to 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS time 24 to 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS time 4 to 2: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS time 6 to 2: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS time 8 to 2: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS time 24 to 2: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS time 6 to 4: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS time 8 to 4: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS time 24 to 4: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS time 8 to 6: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS time 24 to 6: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group LPS time 24 to 8: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group untreated time 8 to 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group untreated time 24 to 0: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
#> Comparing group untreated time 24 to 8: keeping 100 of 100 features (100.0%)
#> Warning: Zero sample variances detected, have been offset away from zero
plot_DE_between_time(DE_between_time_out,
    fontsize = 8, value = TRUE, nrow = 1, heatmap_width = 3)