search

DimmestP / chimera_project_manuscript

1 stars 2 forks source link

Add figure comparing fluorescence with RT-qPCR for motif constructs #110

Closed ewallace closed 3 years ago

ewallace commented 3 years ago

We had this figure, then it was taken out again, and we still need it (probably as supplementary).

What's happening and how are we we going to fix it?

DimmestP commented 3 years ago

Something like this? Similar to figure 1C

RPS3_TSA1_PIR1_protein_and_RNA_plot

ewallace commented 3 years ago

Wow! It's surprising how the substitutions in PIR1 increase the protein level while mildly decreasing the RNA level.

Yes, something like this. I suggest putting these side to side and making the PIR1 figure taller, so it can have a different "portrait" aspect ratio while maintaining coord_equal. Also it would be nice to get something to differentiate the points better, e.g. shape as well as colour?

If you tell me where this is on which branch, I could play around, or you could upgrade it?

DimmestP commented 3 years ago

Just pushed a protein_vs_RNA_motif_plot branch

DimmestP commented 3 years ago

The file is in raw_data_analysis/code/raw_platereader_analysis/motif_context_dependence/RPS3_PIR1_TSA1_protein_vs_RNA_abund.Rmd

ewallace commented 3 years ago

I made these updates but we have to redo the plot from the ground up anyway (see below after image). image

This version plots a point for each biological replicate. That is not appropriate because the protein abundance (by plate reader) was a separate set of experiments from the RNA abundance (by qPCR), so there is no reason to pair "biorep 1" of protein data with "biorep 1" from RNA data. It's misleading as-is.

It would be more appropriate to do a star plot with point estimate and confidence intervals for each construct. Given that we already plot those for the qPCR data in qPCR_model_coef_and_pred_vs_exp_abund.png, why not include the protein summary statistics and make this plot as part of the hlife_motif_pred_vs_qpcr_abund.Rmd script?

ewallace commented 3 years ago

I think @DimmestP put together a nice new figure; we need to replace (current) Figure S1 with this.

ewallace commented 3 years ago

Ready to close, fixed by #154.