annotate wgcna_eigengene_visualization.Rmd @ 6:05bcad4b5b4f draft default tip

minor fix function missing issue

---
title: 'WGCNA: eigengene visualization'
output:
    html_document:
      number_sections: true
      toc: true
      theme: cosmo
      highlight: tango
---

```{r setup, include=FALSE, warning=FALSE, message=FALSE}
knitr::opts_chunk$set(
  echo = ECHO
)
```

# Import workspace 

This step imports workspace from the **WGCNA: construct network** step.

```{r}
fcp = file.copy("CONSTRUCT_NETWORK_WORKSPACE", "deseq.RData")
load("deseq.RData")
```


# Gene modules {.tabset}

```{r}
if(!is.na(SOFT_THRESHOLD_POWER)) soft_threshold_power = SOFT_THRESHOLD_POWER
```

## Identify gene modules

The gene network is constructed based on **soft threshold power = `r soft_threshold_power`**

```{r}
gene_network = blockwiseModules(expression_data, power = soft_threshold_power,
                                TOMType = "unsigned", minModuleSize = 30,
                                reassignThreshold = 0, mergeCutHeight = 0.25,
                                numericLabels = TRUE, pamRespectsDendro = FALSE,
                                verbose = 3)
```


```{r}
modules = table(gene_network$colors)
n_modules = length(modules) - 1
module_size_upper = modules[2]
module_size_lower = modules[length(modules)]

module_table = data.frame(model_label = c(0, 1:n_modules),
                          gene_size = as.vector(modules))
datatable(t(module_table))
```

The results above indicates that there are **`r n_modules` gene modules**, labeled 1 through `r length(n_modules)` in order of descending size. The largest module has **`r module_size_upper` genes**, and the smallest module has **`r module_size_lower` genes**. The label 0 is reserved for genes outside of all modules. 


## Dendrogram and module plot

```{r}
# Convert labels to colors for plotting
module_colors = labels2colors(gene_network$colors)
# Plot the dendrogram and the module colors underneath
plotDendroAndColors(gene_network$dendrograms[[1]], module_colors[gene_network$blockGenes[[1]]],
                    "Module colors",
                    dendroLabels = FALSE, hang = 0.03,
                    addGuide = TRUE, guideHang = 0.05)
```


# Gene module correlation

We can calculate eigengenes and use them as representative profiles to quantify similarity of found gene modules.

```{r}
n_genes = ncol(expression_data)
n_samples = nrow(expression_data)
```

```{r}
diss_tom = 1-TOMsimilarityFromExpr(expression_data, power = soft_threshold_power)
set.seed(123)
select_genes = sample(n_genes, size = PLOT_GENES)
select_diss_tom = diss_tom[select_genes, select_genes]

# calculate gene tree on selected genes
select_gene_tree = hclust(as.dist(select_diss_tom), method = 'average')
select_module_colors = module_colors[select_genes]

# transform diss_tom with a power to make moderately strong connections more visiable in the heatmap.
plot_diss_tom = select_diss_tom^7
# set diagonal to NA for a nicer plot
diag(plot_diss_tom) = NA
```


```{r fig.align='center'}
TOMplot(plot_diss_tom, select_gene_tree, select_module_colors, main = "Network heatmap")
```


# Eigengene visualization {.tabset}

## Eigengene dendrogram

```{r fig.align='center'}
module_eigengenes = moduleEigengenes(expression_data, module_colors)$eigengenes
plotEigengeneNetworks(module_eigengenes, "Eigengene dendrogram", 
                      plotHeatmaps = FALSE)
```

## Eigengene adjacency heatmap

```{r fig.align='center'}
plotEigengeneNetworks(module_eigengenes, "Eigengene adjacency heatmap", 
                      marHeatmap = c(2, 3, 2, 2),
                      plotDendrograms = FALSE, xLabelsAngle = 90)
```