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@AHuffmyer
AHuffmyer committed Oct 1, 2024
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42 changes: 30 additions & 12 deletions ...0-Preliminary-lipidomic-and-metabolomics-analysis-of-Hawaii-2023-larval-data.md
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Expand Up @@ -617,13 +617,15 @@ permanova<-adonis2(vegan ~ parent*temperature, data = wide_data, method='eu')
permanova
```

```
adonis2(formula = vegan ~ parent * temperature, data = wide_data, method = "eu")
Df SumOfSqs R2 F Pr(>F)
parent 2 3925 0.09312 2.5252 0.024 *
temperature 2 3346 0.07938 2.1525 0.050 *
parent:temperature 4 2238 0.05309 0.7198 0.703
Residual 42 32642 0.77441
Total 50 42150 1.00000
Total 50 42150 1.00000
```

Because the unsupervised analysis shows an effect of parent and temperature, we will proceed with PLSDA analyses to look at VIPS that separate parent groups and those that separate temperature groups.

Expand Down Expand Up @@ -872,13 +874,15 @@ permanova<-adonis2(vegan ~ parent*temperature, data = vip_data_parent, method='e
permanova
```

```
adonis2(formula = vegan ~ parent * temperature, data = vip_data_parent, method = "eu")
Df SumOfSqs R2 F Pr(>F)
parent 2 2631.8 0.22209 7.0674 0.001 ***
temperature 2 874.1 0.07376 2.3472 0.031 *
parent:temperature 4 524.0 0.04422 0.7035 0.753
Residual 42 7820.1 0.65993
Total 50 11850.0 1.00000
Total 50 11850.0 1.00000
```

```
pca_vip_parent1<-ggplot2::autoplot(scaled.pca, data=vip_data_parent, frame.colour="parent", loadings=FALSE, colour="parent", shape="temperature", loadings.label.colour="black", loadings.colour="black", loadings.label=FALSE, frame=TRUE, loadings.label.size=5, loadings.label.vjust=-1, size=4) +
Expand Down Expand Up @@ -1107,13 +1111,16 @@ permanova<-adonis2(vegan ~ parent*temperature, data = vip_data_temperature, meth
permanova
```

```
adonis2(formula = vegan ~ parent * temperature, data = vip_data_temperature, method = "eu")
Df SumOfSqs R2 F Pr(>F)
parent 2 1228.1 0.09786 2.7436 0.018 *
temperature 2 1219.2 0.09715 2.7237 0.021 *
parent:temperature 4 702.6 0.05598 0.7848 0.681
Residual 42 9400.1 0.74901
Total 50 12550.0 1.00000
Total 50 12550.0 1.00000
```

```
pca_vip_temperature1<-ggplot2::autoplot(scaled.pca, data=vip_data_temperature, frame.colour="parent", loadings=FALSE, colour="parent", shape="temperature", loadings.label.colour="black", loadings.colour="black", loadings.label=FALSE, frame=TRUE, loadings.label.size=5, loadings.label.vjust=-1, size=4) +
Expand Down Expand Up @@ -1350,13 +1357,15 @@ permanova<-adonis2(vegan ~ parent*temperature, data = vip_data_interaction, meth
permanova
```

```
adonis2(formula = vegan ~ parent * temperature, data = vip_data_interaction, method = "eu")
Df SumOfSqs R2 F Pr(>F)
parent 2 2779.5 0.18407 5.8640 0.001 ***
temperature 2 1432.4 0.09486 3.0220 0.002 **
parent:temperature 4 934.5 0.06189 0.9858 0.450
Residual 42 9953.7 0.65918
Total 50 15100.0 1.00000
Total 50 15100.0 1.00000
```

No interactive effect detected.

Expand Down Expand Up @@ -1429,7 +1438,7 @@ full_lipid_list<-lipids_filtered%>%

What is the overlap in these lists? Create an upset plot.

```{r}
```
# Combine lists into a data frame indicating membership (1 = present, 0 = absent)
upset_data <- data.frame(
Lipid = unique(c(parent_vip_list, temperature_vip_list, interaction_vip_list)),
Expand Down Expand Up @@ -1559,7 +1568,7 @@ Heatmap of parent VIPs:

PCA of parent VIPs:

![](https://github.com/AHuffmyer/ASH_Putnam_Lab_Notebook/blob/master/images/NotebookImages/Hawaii2023/omics/pca_plots_parentVIP_height.png?raw=true)
![](https://github.com/AHuffmyer/ASH_Putnam_Lab_Notebook/blob/master/images/NotebookImages/Hawaii2023/omics/pca_plots_parentVIP_height.jpeg?raw=true)

## Temperature effects

Expand Down Expand Up @@ -2242,13 +2251,15 @@ permanova<-adonis2(vegan ~ parent*temperature, data = wide_data, method='eu')
permanova
```

```
adonis2(formula = vegan ~ parent * temperature, data = wide_data, method = "eu")
Df SumOfSqs R2 F Pr(>F)
parent 2 79.95 0.03203 0.8623 0.483
temperature 2 74.27 0.02975 0.8009 0.542
parent:temperature 4 301.81 0.12092 1.6274 0.087 .
Residual 44 2039.97 0.81730
Total 52 2496.00 1.00000
Total 52 2496.00 1.00000
```

No effect of parent or temperature.

Expand Down Expand Up @@ -2292,7 +2303,7 @@ Script modified from the following tutorial: https://mixomicsteam.github.io/Book

### PLS-DA for the effect of parent

Generate a PLS-DA and plot.
Generate a PLS-DA and plot.

```
#assigning datasets
Expand Down Expand Up @@ -2323,7 +2334,7 @@ plotIndiv(MyResult.plsda, col=cols, ind.names = FALSE, legend=TRUE, legend.title

Set model to determine VIPs.

```{r, message=FALSE}
```
MyResult.plsda_parent <- plsda(X,Y, ncomp=2)
#view plsda model again
Expand Down Expand Up @@ -2483,13 +2494,15 @@ permanova<-adonis2(vegan ~ parent*temperature, data = vip_data_parent, method='e
permanova
```

```
adonis2(formula = vegan ~ parent * temperature, data = vip_data_parent, method = "eu")
Df SumOfSqs R2 F Pr(>F)
parent 2 44.50 0.05705 1.5591 0.182
temperature 2 22.15 0.02839 0.7760 0.548
parent:temperature 4 85.45 0.10955 1.4969 0.159
Residual 44 627.91 0.80501
Total 52 780.00 1.00000
Total 52 780.00 1.00000
```

No difference in VIPs by parent or temperature.

Expand Down Expand Up @@ -2719,13 +2732,15 @@ permanova<-adonis2(vegan ~ parent*temperature, data = vip_data_temperature, meth
permanova
```

```
adonis2(formula = vegan ~ parent * temperature, data = vip_data_temperature, method = "eu")
Df SumOfSqs R2 F Pr(>F)
parent 2 28.82 0.05543 1.5314 0.208
temperature 2 23.68 0.04553 1.2579 0.263
parent:temperature 4 53.42 0.10273 1.4192 0.203
Residual 44 414.08 0.79630
Total 52 520.00 1.00000
Total 52 520.00 1.00000
```

No significant effects.

Expand Down Expand Up @@ -2758,6 +2773,7 @@ pca_plots_temperature<-plot_grid(pca_vip_temperature1, pca_vip_temperature2, nco
ggsave(pca_plots_temperature, filename="figures/metabolites/pca_plots_temperatureVIP.jpeg", width=12, height=4)
```

![](https://github.com/AHuffmyer/ASH_Putnam_Lab_Notebook/blob/master/images/NotebookImages/Hawaii2023/omics/metabolomics/pca_plots_temperatureVIP.jpeg?raw=true)

### PLS-DA for the effect of parent x temperature groups
Expand Down Expand Up @@ -2959,13 +2975,15 @@ permanova<-adonis2(vegan ~ parent*temperature, data = vip_data_interaction, meth
permanova
```

```
adonis2(formula = vegan ~ parent * temperature, data = vip_data_interaction, method = "eu")
Df SumOfSqs R2 F Pr(>F)
parent 2 28.06 0.04151 1.1445 0.332
temperature 2 27.70 0.04098 1.1299 0.315
parent:temperature 4 80.85 0.11960 1.6489 0.099 .
Residual 44 539.39 0.79791
Total 52 676.00 1.00000
Total 52 676.00 1.00000
```

No effects are significant.

Expand Down

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