Fix Barplots Script

[davebridges]

Switch to using FPKM table and repair a script error

[davebridges]

Whats the problem with this? It ran fine on my laptop.

[davebridges]

The updated barplots look great. Can you make the following barplot combinations for me (where they are on the same plot using RPKM as the y-axis). I indicated where they fit in the figures, but you can just call them the gene combinations to make it easier.

• Figure XX: SOCS2/CISH
• Supplementary Figure X: MAPK3/MAPK7/FOS/JUN/JUNB
• Supplementary Figure 1A: PTPN3/PTPN4
• Supplementary Figure 1B: CCNC/CCNE/CDKN2B
• Supplementary Figure 1C: NAP1L1/ORC2/BAG4/CAPN6
• Supplementary Figure 1D: MAP3K5/MAPK14/MAPK13/MAPKAPK3
• Figure 4A: LPL/PNPLA2/LIPE/MGLL (in that order)
• Figure 4B: ABHD5/ADRB3/ACVR1C
• Figure 4C: AACA/ACACA/ACSL3/FASN
• Supplementary Figure 1E: UGP2/PYGM
• Figure 4D: SCD/FADS1/FADS2/CYB5A
• Supplementary Figure 2A: INSR/IRS1/IRS2/AKT1/AKT2/AKT3/SLC2A4
• Supplementary Figure 2B: STAT4/STAT6/IKBKB/IL1B/IL6/MCP1/IKBKE
• Supplementary Figure 2C: HSD11B1/HSD11B2/NR3C1/NR3C2

These may not all fit on the same graphs since its possible their RPKM values will vary by a lot, but lets take a look and then if we have to separate out these groups we can decide after taking a look.

[qtran1]

I made all of the figures that you requested. Let me know if you need anything else.

[davebridges]

They look great, but a few small things:

• Supplementary 1B should also have CCNE1 (that was a typo on me)
• 4C should also have AACA
• 4C you will have to put FASN on separate axes from AACA/ACACA/ACSL3 since the scales are so far off.
• Same with 4D, where you will have to put SCD on a separate axis.

[davebridges]

Also, I need one for IGF/IGFBP3 (Figure 3A).

I think it would be easier to name these barplots with their combined names (like Barplot IGF_IGFBP3) rather than their figures though, since the figure numbers can change a lot.

[davebridges]

It turns out we were wrong about what ACVR1C does, so we are going to need to remove that from that figure, so I'd like to change the lipolytic regulator figure should to have ABHD5/ADRB1/ADRB2/ADRB3 (if they scale ok).

[qtran1]

Everything was addressed excel that I can't find AACA.

[davebridges]

AACS, sorry