UC Berkeley-LBNL
This GitHub is to show all the scripts that were made in the research project on the effect of Trichoderma atroviride exudates on 4 bacteria of the rhizosphere. These are analyzes on BarSeq results performed in the lab of Dr. Adam Deutschbauer and Dr. Louise Glass. These scripts are executed once the fitness tables are received, which have already been deposited in the fitness browser for internal use https://fit.genomics.lbl.gov/. For each of the 4 bacteria in which the interaction experiments were performed and with some drugs.
Script 1. Scatter plot of Klesiella with spent media of WT-Trichoderma:
https://github.com/jmvillalobos/BarSeq-Bacteria-Trichoderma/blob/main/script_scatter_WTKlebciella.R
Negative fitness: 47 Possitive fitness: 0 Recovered: 11
Script 2. Scatter plot of Klesiella with spent media of Dcr2 mutant-Trichoderma:
https://github.com/jmvillalobos/BarSeq-Bacteria-Trichoderma/blob/main/script_scatter_Dcr2Klebciella.R
Negative fitness: 16 Possitive fitness: 0 Recovered: 12
Script 3. Scatter plot of Klesiella with spent media of Tmk3 mutant-Trichoderma:
Negative fitness: 15 Possitive fitness: 0 Recovered: 14
Script 4. Generating a heatmap to show the comparison of fitness associated with Klebsiella genes when exposed to exudates from the WT strain and Trichoderma mutants:
Script 5. Scatter plot of Herbaspirillum with spent media of WT-Trichoderma:
https://github.com/jmvillalobos/BarSeq-Bacteria-Trichoderma/blob/main/script_scatter_WTHerbaspirillum.R
Negative fitness: 32 Possitive fitness: 1 Recovered: 4
Script 6. Scatter plot of Herbaspirillum with spent media of Dcr2-Trichoderma:
https://github.com/jmvillalobos/BarSeq-Bacteria-Trichoderma/blob/main/script_scatter_Dcr2Herbaspirillum.R
Negative fitness: 17 Possitive fitness: 0 Recovered: 5
Script 7. Scatter plot of Herbaspirillum with spent media of Tmk3-Trichoderma:
https://github.com/jmvillalobos/BarSeq-Bacteria-Trichoderma/blob/main/script_scatter_Tmk3Herbaspirillum.R
Negative fitness: 17 Possitive fitness: 1 Recovered: 5
Script 8. Generating a heatmap to show the comparison of fitness associated with Herbaspirillum genes when exposed to exudates from the WT strain and Trichoderma mutants:
https://github.com/jmvillalobos/BarSeq-Bacteria-Trichoderma/blob/main/heatmap_Globalfitness_Herbaspirillum.R
Script 9. Scatter plot of Herbaspirillum with spent media of WT-Trichoderma:
https://github.com/jmvillalobos/BarSeq-Bacteria-Trichoderma/blob/main/script_scatter_WTSimiae.R
Negative fitness: 38 Possitive fitness: 10 Recovered: 3
Script 10. Scatter plot of Pseudomonas simiae with spent media of Dcr2-Trichoderma:
https://github.com/jmvillalobos/BarSeq-Bacteria-Trichoderma/blob/main/script_scatter_Dcr2Simiae.R
Negative fitness: 4 Possitive fitness: 0 Recovered: 8
Script 11. Scatter plot of Pseudomonas simiae with spent media of Tmk3-Trichoderma:
https://github.com/jmvillalobos/BarSeq-Bacteria-Trichoderma/blob/main/script_scatter_Tmk3Simiae.R
Negative fitness: 27 Possitive fitness: 5 Recovered: 7
Script 12. Generating a heatmap to show the comparison of fitness associated with Pseudomonas simiae genes when exposed to exudates from the WT strain and Trichoderma mutants:
https://github.com/jmvillalobos/BarSeq-Bacteria-Trichoderma/blob/main/heatmap_Globalfitness_PSimiae.R
Script 13. Scatter plot of Pseudomonas putida with spent media of WT-Trichoderma:
https://github.com/jmvillalobos/BarSeq-Bacteria-Trichoderma/blob/main/script_scatter_WTPutida.R
Negative fitness: 40 Possitive fitness: 1 Recovered: 1
Script 14. Scatter plot of Pseudomonas putida with spent media of Dcr2-Trichoderma:
https://github.com/jmvillalobos/BarSeq-Bacteria-Trichoderma/blob/main/script_scatter_Dcr2Putida.R
Negative fitness: 27 Possitive fitness: 12 Recovered: 3
Script 15. Scatter plot of Pseudomonas putida with spent media of Tmk3-Trichoderma:
https://github.com/jmvillalobos/BarSeq-Bacteria-Trichoderma/blob/main/script_scatter_Tmk3Putida.R
Negative fitness: 38 Possitive fitness: 4 Recovered: 1
Script 16. Generating a heatmap to show the comparison of fitness associated with Pseudomonas putida KT2440 genes when exposed to exudates from the WT strain and Trichoderma mutants:
https://github.com/jmvillalobos/BarSeq-Bacteria-Trichoderma/blob/main/heatmap_Globalfitness_PPutida.R
BarSeq-Effect on Pseudomonas bacteria of pure toxins (Polymyxin B and Fusaric acid) at different concentrations.
Script 17. 0.003 mg/ml: https://github.com/jmvillalobos/BarSeq-Bacteria-Trichoderma/blob/main/script_scatterSimiae_poly0.003.R
Negative fitness: 119 Possitive fitness: 54 Recovered: 3
Script 18. 0.002 mg/ml: https://github.com/jmvillalobos/BarSeq-Bacteria-Trichoderma/blob/main/script_scatterSimiae_poly0.002.R
Negative fitness: 57 Possitive fitness: 23 Recovered: 0
Script 19. FA 120 ug/ml: https://github.com/jmvillalobos/BarSeq-Bacteria-Trichoderma/blob/main/script_scatter_SimiaeFus120.R
Negative fitness: 45 Possitive fitness: 15 Recovered: 4
Script 20. 0.001 mg/ml: https://github.com/jmvillalobos/BarSeq-Bacteria-Trichoderma/blob/main/script_scatterPutida_poly0.001.R
Script 21. 0.002 mg/ml: https://github.com/jmvillalobos/BarSeq-Bacteria-Trichoderma/blob/main/script_scatterPutida_poly0.002.R
Script 22. Fusaric acid 480, 240 and 120 ug/ml: https://github.com/jmvillalobos/BarSeq-Bacteria-Trichoderma/blob/main/script_scatter_PutidaFus480%2C240%26120ug:ml.R