A wrapper function which calls the necessary functions to create a heatmap illustrating the significant DEGs of a given differential expression type (DE_type)

custom_heatmap_wrapper(
  time_object,
  DE_type,
  log_transform = TRUE,
  plot_file_name = "custom_DEG_heatmap",
  adjust_missing_temp_samples = TRUE,
  do_SVGs = TRUE
)

Arguments

time_object

A time object

DE_type

The type of heatmap being created (conditional or temporal)

log_transform

Boolean indicating if the results should be log transformed on the heatmap

plot_file_name

The file name to be given to the heatmap once it is saved

adjust_missing_temp_samples

Boolean indicating if missing temporal samples should be compensated for (NA introduced). Currently, there is no reason to have this set to False.

do_SVGs

Boolean indicating if SVG files should be saved for the heatmaps

Value

none or heatmap plot

Examples

TS_object<-create_example_object_for_R()
TS_object <- normalize_timeSeries_with_deseq2(time_object=TS_object)
#> converting counts to integer mode
#Perform conditional differential gene expression analysis
TS_object<-conditional_DE_wrapper(TS_object,vignette_run=TRUE)
heat_plot<-custom_heatmap_wrapper(TS_object,DE_type='conditional',log_transform=TRUE,
                                  plot_file_name = NULL,
                                  adjust_missing_temp_samples=TRUE,do_SVGs=FALSE)