ipRGC TRAP vs. bulk – Compare the trap and bulk results.

1 Introduction

Collect the results from the gene/tx TRAP and bulk analyses here and perform a few AUCC/correlation/etc comparisons to see how similar/different they are.

*** Reminder to myself ***

When I did this on my main computer, I had the same environment loaded for the bulk and trap data. In the container this is not possible; so I will need to judiciously use the rda argument to combine_de_tables() and collect up the results before running the following blocks. Don’t forget to add that.

2 Compare the bulk and TRAP data

There are a few variables from the bulk analyses which we may use to compare to the TRAP data:

mm_de_dlgn_sva, mm_de_ret_sva, mm_de_scn_sva, mm_de_dlgn, mm_de_ret, mm_de_scn.

Those are location-specific contrasts.

genoloc_de_sva/genoloc_table_sva provide all contrasts that I thought might be fun.

The following is all pre-wt filtering. Next I will repeat everything post-filtering.

## The bulk tables
genoloc_table_sva[["table_names"]]

## The TRAP tables
location_tables_full[["table_names"]]
genotype_tables_full[["table_names"]]
time_tables_full[["table_names"]]

## Retina het vs Retina wt
bulk_table <- genoloc_table_sva[["data"]][["Retina_ko_vs_Retina_het"]]
trap_table <- genotype_tables_full[["data"]][["kh_p08_retina"]]
retina_ko_het_aucc <- calculate_aucc(bulk_table, trap_table,
                                     px = "deseq_adjp", py = "deseq_adjp",
                                     lx = "deseq_logfc", ly = "deseq_logfc")
retina_ko_het_aucc
retina_ko_het_ros <- rank_order_scatter(bulk_table, trap_table)
retina_ko_het_ros[["lfc_scatter"]]

bulk_table <- genoloc_table_sva[["data"]][["Retina_ko_vs_Retina_het"]]
trap_table <- genotype_tables_full[["data"]][["kh_p15_retina"]]
retina_ko_het_aucc <- calculate_aucc(bulk_table, trap_table,
                                     px = "deseq_adjp", py = "deseq_adjp",
                                     lx = "deseq_logfc", ly = "deseq_logfc")
retina_ko_het_aucc
retina_ko_het_ros <- rank_order_scatter(bulk_table, trap_table)
retina_ko_het_ros[["lfc_scatter"]]

bulk_table <- genoloc_table_sva[["data"]][["SCN_ko_vs_SCN_het"]]
trap_table <- genotype_tables_full[["data"]][["kh_p08_scn"]]
scn_ko_het_aucc <- calculate_aucc(bulk_table, trap_table,
                                     px = "deseq_adjp", py = "deseq_adjp",
                                     lx = "deseq_logfc", ly = "deseq_logfc")
scn_ko_het_aucc
scn_ko_het_ros <- rank_order_scatter(bulk_table, trap_table)
scn_ko_het_ros[["lfc_scatter"]]


bulk_table <- genoloc_table_sva[["data"]][["SCN_ko_vs_SCN_het"]]
trap_table <- genotype_tables_full[["data"]][["kh_p15_scn"]]
scn_ko_het_aucc <- calculate_aucc(bulk_table, trap_table,
                                     px = "deseq_adjp", py = "deseq_adjp",
                                     lx = "deseq_logfc", ly = "deseq_logfc")
scn_ko_het_aucc
scn_ko_het_ros <- rank_order_scatter(bulk_table, trap_table)
scn_ko_het_ros[["lfc_scatter"]]

bulk_table <- genoloc_table_sva[["data"]][["dLGN_ko_vs_dLGN_het"]]
trap_table <- genotype_tables_full[["data"]][["kh_p08_dlgn"]]
dlgn_ko_het_aucc <- calculate_aucc(bulk_table, trap_table,
                                     px = "deseq_adjp", py = "deseq_adjp",
                                     lx = "deseq_logfc", ly = "deseq_logfc")
dlgn_ko_het_aucc
dlgn_ko_het_ros <- rank_order_scatter(bulk_table, trap_table)
dlgn_ko_het_ros[["lfc_scatter"]]

bulk_table <- genoloc_table_sva[["data"]][["dLGN_ko_vs_dLGN_het"]]
trap_table <- genotype_tables_full[["data"]][["kh_p15_dlgn"]]
dlgn_ko_het_aucc <- calculate_aucc(bulk_table, trap_table,
                                     px = "deseq_adjp", py = "deseq_adjp",
                                     lx = "deseq_logfc", ly = "deseq_logfc")
dlgn_ko_het_aucc
dlgn_ko_het_ros <- rank_order_scatter(bulk_table, trap_table)
dlgn_ko_het_ros[["lfc_scatter"]]

## The bulk tables
genoloc_table_sva[["table_names"]]

## The TRAP tables
location_tables[["table_names"]]
genotype_tables[["table_names"]]
time_tables[["table_names"]]

## Retina het vs Retina wt
bulk_table <- genoloc_table_sva[["data"]][["Retina_ko_vs_Retina_het"]]
trap_table <- genotype_tables_full[["data"]][["kh_p08_retina"]]
retina_ko_het_aucc <- calculate_aucc(bulk_table, trap_table,
                                     px = "deseq_adjp", py = "deseq_adjp",
                                     lx = "deseq_logfc", ly = "deseq_logfc")
retina_ko_het_aucc
retina_ko_het_ros <- rank_order_scatter(bulk_table, trap_table)
retina_ko_het_ros[["lfc_scatter"]]

bulk_table <- genoloc_table_sva[["data"]][["Retina_ko_vs_Retina_het"]]
trap_table <- genotype_tables_full[["data"]][["kh_p15_retina"]]
retina_ko_het_aucc <- calculate_aucc(bulk_table, trap_table,
                                     px = "deseq_adjp", py = "deseq_adjp",
                                     lx = "deseq_logfc", ly = "deseq_logfc")
retina_ko_het_aucc
retina_ko_het_ros <- rank_order_scatter(bulk_table, trap_table)
retina_ko_het_ros[["lfc_scatter"]]

bulk_table <- genoloc_table_sva[["data"]][["SCN_ko_vs_SCN_het"]]
trap_table <- genotype_tables_full[["data"]][["kh_p08_scn"]]
scn_ko_het_aucc <- calculate_aucc(bulk_table, trap_table,
                                     px = "deseq_adjp", py = "deseq_adjp",
                                     lx = "deseq_logfc", ly = "deseq_logfc")
scn_ko_het_aucc
scn_ko_het_ros <- rank_order_scatter(bulk_table, trap_table)
scn_ko_het_ros[["lfc_scatter"]]


bulk_table <- genoloc_table_sva[["data"]][["SCN_ko_vs_SCN_het"]]
trap_table <- genotype_tables_full[["data"]][["kh_p15_scn"]]
scn_ko_het_aucc <- calculate_aucc(bulk_table, trap_table,
                                     px = "deseq_adjp", py = "deseq_adjp",
                                     lx = "deseq_logfc", ly = "deseq_logfc")
scn_ko_het_aucc
scn_ko_het_ros <- rank_order_scatter(bulk_table, trap_table)
scn_ko_het_ros[["lfc_scatter"]]

bulk_table <- genoloc_table_sva[["data"]][["dLGN_ko_vs_dLGN_het"]]
trap_table <- genotype_tables_full[["data"]][["kh_p08_dlgn"]]
dlgn_ko_het_aucc <- calculate_aucc(bulk_table, trap_table,
                                     px = "deseq_adjp", py = "deseq_adjp",
                                     lx = "deseq_logfc", ly = "deseq_logfc")
dlgn_ko_het_aucc
dlgn_ko_het_ros <- rank_order_scatter(bulk_table, trap_table)
dlgn_ko_het_ros[["lfc_scatter"]]

bulk_table <- genoloc_table_sva[["data"]][["dLGN_ko_vs_dLGN_het"]]
trap_table <- genotype_tables_full[["data"]][["kh_p15_dlgn"]]
dlgn_ko_het_aucc <- calculate_aucc(bulk_table, trap_table,
                                     px = "deseq_adjp", py = "deseq_adjp",