updated integrate annotation and report

[MahdiMoradiMarjaneh]

Updates include:

• added Sankey plot (riverplot) feature to the integrate report (Amend the LIGER report: (1) implement the hexogonal tSNE plots into the LIGER report, (2) get the riverplot into the LIGER report, (3) in the LIGER report, in the Clustering section, show bar plots with percentage of each cluster that comes from each group variable. #144)
• added proportional barplot feature to the integrate report showing what percentage of each cluster comes from each group variable (Amend the LIGER report: (1) implement the hexogonal tSNE plots into the LIGER report, (2) get the riverplot into the LIGER report, (3) in the LIGER report, in the Clustering section, show bar plots with percentage of each cluster that comes from each group variable. #144)
• fixed issue store cluster labels for each reduction_method #142. Labels in clustering plots generated by annotate_integrated_sce() now reflect the correct reduction_method used in cluster_sce()
• minor updates to liger_preprocess()

List of file changes:

modified:   R/annotate_integrated_sce.R
modified:   R/liger_preprocess.R
modified:   R/report_integrated_sce.R
new file:   inst/rmarkdown/templates/integrate/skeleton/categorical_covariates_2.Rmd
modified:   inst/rmarkdown/templates/integrate/skeleton/skeleton.Rmd