R/DE_PART_results_functions.R
custom_heatmap_wrapper.Rd
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
)
A time object
The type of heatmap being created (conditional or temporal)
Boolean indicating if the results should be log transformed on the heatmap
The file name to be given to the heatmap once it is saved
Boolean indicating if missing temporal samples should be compensated for (NA introduced). Currently, there is no reason to have this set to False.
Boolean indicating if SVG files should be saved for the heatmaps
none or heatmap plot
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)