---
title: "Population genetic analysis with tidypopgen"
output: rmarkdown::html_vignette
        #pdf_document
vignette: >
  %\VignetteIndexEntry{Population genetic analysis with tidypopgen}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
set.seed(123)
```


## An example workflow with real data
We will explore the genetic structure of *Anolis punctatus* in South America,
using data from Prates et al 2018. We downloaded the vcf file of the genotypes
from "https://github.com/ivanprates/2018_Anolis_EcolEvol/blob/master/data/VCFtools_SNMF_punctatus_t70_s10_n46/punctatus_t70_s10_n46_filtered.recode.vcf?raw=true" and compressed it to a vcf.gz file.

We read in the data from the compressed vcf with:
```{r}
library(tidypopgen)
vcf_path <-
  system.file("/extdata/anolis/punctatus_t70_s10_n46_filtered.recode.vcf.gz",
    package = "tidypopgen"
  )
anole_gt <-
  gen_tibble(vcf_path, quiet = TRUE, backingfile = tempfile("anolis_"))
```

Now let's inspect our `gen_tibble`:
```{r}
anole_gt
```

We can see that we have 46 individuals, from 3249 loci. Note that we don't have
any information on population from the vcf. That information can be found from
another csv file. We will have add the population information manually. Let's
start by reading the
file:
```{r}
pops_path <- system.file("/extdata/anolis/punctatus_n46_meta.csv",
  package = "tidypopgen"
)
pops <- read.csv(pops_path)
pops
```

We can now attempt to join the tables. We recommend using a `left_join` to do
so, rather than `cbind` or `bind_cols`, as the latter functions assume that
the two tables are in the same order. In this case, we do not want to bring
over the wrong data due to mismatched ordering.

```{r, error=TRUE}
anole_gt <- anole_gt %>% left_join(pops, by = "id")
```

Let us check that we have been successful:
```{r}
anole_gt %>% glimpse()
```

## Map

Lets begin by visualising our samples geographically. We have latitudes and
longitudes in our tibble; we can transform them into an `sf` geometry with the 
function `gt_add_sf()`. Once we have done that, our `gen_tibble` will act as
an `sf` object, which can be plotted with `ggplot2`.

```{r}
anole_gt <- gt_add_sf(anole_gt, c("longitude", "latitude"))
anole_gt
```

To visualise our samples, we can create a map of South America using the
`rnaturalearth` package. We will use the `ne_countries()` function to get
the countries in South America. We will then plot the map and add our samples
using the `geom_sf()` function from `ggplot2`.

```{r}
library(rnaturalearth)
library(ggplot2)

map <- ne_countries(
  continent = "South America",
  type = "map_units", scale = "medium"
)

ggplot() +
  geom_sf(data = map) +
  geom_sf(data = anole_gt$geometry) +
  coord_sf(
    xlim = c(-85, -30),
    ylim = c(-30, 15)
  ) +
  theme_minimal()
```

From our map we can see that we have samples from the coastal Atlantic Forest and the Amazonian
Forest.

## PCA

That was easy. The loci had already been filtered and cleaned, so we don't need 
to do any QC. Let us jump straight into analysis and run a PCA:
```{r, error=TRUE}
anole_pca <- anole_gt %>% gt_pca_partialSVD(k = 30)
```
OK, we jumped too quickly. There are missing data, and we need first 
to impute them:

```{r}
anole_gt <- gt_impute_simple(anole_gt, method = "mode")
```

And now:
```{r}
anole_pca <- anole_gt %>% gt_pca_partialSVD(k = 30)
```

Let us look at the object:
```{r}
anole_pca
```

The `print` function (implicitly called when we type the name of the object)
gives us information about the most important elements in the object (and the names
of the elements in which they are stored).

We can extract those elements with the `tidy` function, which returns a tibble
that can be easily used for further analysis, e.g.:
```{r}
tidy(anole_pca, matrix = "eigenvalues")
```
We can return information on the *eigenvalues*, *scores* and *loadings* of the pca.
There is also an `autoplot` method that allows to visualise those elements (type *screeplot* for
*eigenvalues*, type *scores* for *scores*, and *loadings* for *loadings*:
```{r, fig.alt = "Scree Plot of eigenvalues for each Principal Component"}
autoplot(anole_pca, type = "screeplot")
```

To plot the sample in principal coordinates space, we can simply use:
```{r, fig.alt = "Score plot of individuals across the first and second Principal Components"}
autoplot(anole_pca, type = "scores")
```

`autoplots` are deliberately kept simple: they are just a way to quickly inspect the results.
They generate `ggplot2` objects, and so they can be further embellished with the usual
`ggplot2` grammar:
```{r, fig.alt = "Score plot of individuals across the first and second Principal Components, with individual samples coloured by population"}
library(ggplot2)
autoplot(anole_pca, type = "scores") +
  aes(color = anole_gt$population) +
  labs(color = "population")
```

For more complex/publication ready plots, we will want to add the PC scores
to the tibble, so that we can create a custom plot with `ggplot2`. We can easily
add the data with the `augment` method:

```{r}
anole_gt <- augment(anole_pca, data = anole_gt)
```

And now we can use `ggplot2` directly to generate our plot:

```{r, fig.alt = "Another score plot of individuals across the first and second Principal Components, with individual samples coloured by population, using ggplot2"}
anole_gt %>% ggplot(aes(.fittedPC1, .fittedPC2, color = population)) +
  geom_point() +
  labs(x = "PC1", y = "PC2", color = "Population")
```

We can see that the two population separate clearly in the PCA space, with individuals
from the Atlantic Forest clustering closely together while Amazonian Forest individuals
are spread across the first two principal components.

It is also possible to inspect which loci contribute the most to a given component:

```{r, fig.alt = "Plot of the loadings of Principal Component 1 for each loci"}
autoplot(anole_pca, type = "loadings")
```

By using information from the loci table, we could easily embellish the plot, for example
colouring by chromosome or maf.

For more complex plots, we can augment the loci table with the loadings using `augment_loci()`:

```{r}
anole_gt_load <- augment_loci(anole_pca, data = anole_gt)
```

# Explore population structure with DAPC

DAPC is a powerful tool to investigate population structure. It has the advantage of
scaling well to very large datasets. It does not have the assumptions of STRUCTURE or
ADMIXTURE (which also limits its power).

The first step is to determine the number of genetic clusters in the dataset. 
DAPC can be either used to test a a-priori hypothesis, or we can use the data to
suggest the number of clusters.
In this case, we did not have any strong expectations of structure in our study system, so we will
let the data inform the number of possible genetic clusters. We will use
a k-clustering algorithm applied to the principal components (allowing us to reduce
the dimensions from the thousands of loci to just a few tens of components). We need to decide how 
many components to use; this decision is often made based on a plot of the cumulative
explained variance of the components.
Using `tidy` on the `gt_pca` object allows us easily obtain those quantities, and it is then
trivial to plot them:
```{r, fig.alt = "Plot of the cumulative loadings for each Principal Component"}
library(ggplot2)
tidy(anole_pca, matrix = "eigenvalues") %>%
  ggplot(mapping = aes(x = PC, y = cumulative)) +
  geom_point()
```

Note that, as we were working with a truncated SVD algorithm for our PCA, we can not easily
phrase the eigenvalues in terms of proportion of total variance, so the cumulative y axis simply
shows the cumulative sum of the eigenvalues. Ideally, we are looking for the point where 
the curve starts flattening. In this case, we can
not see a very clear flattening, but by PC 10 the increase in explained variance has markedly
decelerated. We can now find clusters based on those 10 PCs:

```{r}
anole_clusters <- gt_cluster_pca(anole_pca, n_pca = 10)
```

As we did not define the *k* values to explore, the default 1 to 5 was used (we
can change that by setting the `k` parameter to change the range). To choose an appropriate
*k*, we plot the number of clusters against a measure of fit. BIC has been shown
to be a very good metric under many scenarios:
```{r, fig.alt = "Plot of BIC (Bayesian Information Criteria) for each value of k"}
autoplot(anole_clusters)
```

We are looking for the minimum value of BIC. There is no clear elbow (a minimum
after which BIC increases with increasing k). However, we notice that there is a
quick levelling off in the decrease in BIC at 3 clusters. Arguably, these are
sufficient to capture the main structure. We can also use a number of
algorithmic approaches (based on the original `find.clusters()` function in
`adegenet`) to choose the best *k* value from this plot through
`gt_cluster_pca_best_k()`. We will use the defaults (BIC with "diffNgroup", see
the help page for `gt_cluster_pca_best_k()` for a description of the various
options):
```{r}
anole_clusters <- gt_cluster_pca_best_k(anole_clusters)
```
The algorithm confirms our choice. Note that this function simply adds an element
`$best_k` to the `gt_cluster_pca` object:
```{r}
anole_clusters$best_k
```
If we decided that we wanted to explore a different value, we could simply overwrite
that number with `anole_clusters$best_k<-5`

In this case, we are happy with the option of 3 clusters, and we can run a DAPC:
```{r}
anole_dapc <- gt_dapc(anole_clusters)
```

Note that `gt_dapc()` takes automatically the number of clusters from the `anole_clusters` object,
but can change that behaviour by setting some of its parameters (see the help
page for `gt_dapc()`). When we print the object, we are given information about
the most important elements of the object and where to find them (as we saw for `gt_pca`):

```{r}
anole_dapc
```

Again, these elements can be obtained with tidiers (with `matrix` equal to `eigenvalues`,
`scores`,`ld_loadings` and `loci_loadings`):
```{r}
tidy(anole_dapc, matrix = "eigenvalues")
```

And they can be visualised with `autoplot`:
```{r, fig.alt = "Scree plot of the eigenvalues on the two discriminant axes (defined by `ld`)"}
autoplot(anole_dapc, type = "screeplot")
```

As for pca, there is a `tidy` method that can be used to extract information
from `gt_dapc` objects. For example, if we want to create a bar plot of
the eigenvalues (since we only have two), we could simply use:
```{r, fig.alt = "Bar plot of eigenvalues against the two discriminant axes"}
tidy(anole_dapc, matrix = "eigenvalues") %>%
  ggplot(aes(x = LD, y = eigenvalue)) +
  geom_col()
```

We can plot the scores with:
```{r, fig.alt = "Scatterplot of the scores of each individual on the two discriminant axes (defined by `ld`)"}
autoplot(anole_dapc, type = "scores")
```

The DAPC plot shows the separation of individuals into 3 clusters.

We can inspect this assignment by DAPC with `autoplot` using the type
`components`, ordering the samples by their original population labels:

```{r, fig.alt = "Bar plot showing the probability of assignment to each cluster"}
autoplot(anole_dapc, type = "components", group = anole_gt$population)
```

Here we can see that DAPC splits the Amazonian Forest individuals into two clusters.
Because of the very clear separation we observed when plotting the LD scores,
no individual is modelled as a mixture: all assignments are with 100% probability 
to a single cluster.

Finally, we can explore which loci have the biggest impact on separating the clusters
(either because of drift or selection):

```{r, fig.alt = "Plot of the loadings of Principal Component 1 for each loci"}
autoplot(anole_dapc, "loadings")
```

There is no strong outlier, suggesting drift across many loci has created the signal
picked up by DAPC.

Note that `anole_dapc` is of class `gt_dapc`, which is a subclass of `dapc` 
from `adegenet`. This means that functions written to work on `dapc` objects
should work out of the box (the only exception is `adegenet::predict.dapc`, 
which does not work because the underlying pca object is different). For example,
we can obtain the standard dapc plot with:
```{r, fig.alt = "Scatterplot of individuals with ellipses surrounding each cluster of individuals identified by the DAPC analysis. Eigenvalues are displayed in an inset in the bottom right corner of the plot."}
library(adegenet)
scatter(anole_dapc, posi.da = "bottomright")
```

We can also plot these results onto the map we created earlier.

```{r}
anole_gt <- anole_gt %>% mutate(dapc = anole_dapc$grp)

ggplot() +
  geom_sf(data = map) +
  geom_sf(data = anole_gt$geometry, aes(color = anole_gt$dapc)) +
  coord_sf(
    xlim = c(-85, -30),
    ylim = c(-30, 15)
  ) +
  labs(color = "DAPC cluster") +
  theme_minimal()
```

Atlantic forest lizards form distinct geographic cluster, separate from
the Amazonian lizards.

# Clustering with ADMIXTURE

ADMIXTURE is a fast clustering algorithm which provides results similar to STRUCTURE. 
We can run it directly from tidypopgen using the `gt_admixture` function.

The output of `gt_admixture` is a `gt_admix` object. `gt_admix` objects are designed to make visualising data from different clustering algorithms swift and easy.

Lets begin by running `gt_admixture`. We can run K clusters from k=2 to k=6. 
We will use just one repeat, but ideally we should run multiple repetitions for each K:

```{r, results='hide', echo=TRUE, eval=FALSE}
anole_gt <- anole_gt %>% group_by(population)

anole_adm_original <- gt_admixture(
  x = anole_gt,
  k = 2:6,
  n_runs = 1,
  crossval = TRUE,
  seed = 1
)
```

```{r, results="hide", echo=FALSE, eval=TRUE, warning=FALSE}
anole_gt <- anole_gt %>% group_by(population)

anole_adm <- readRDS("a03_anole_adm.rds")
```

Note that within this vignette we are not running the `gt_admixture` function,
as it requires the ADMIXTURE software to be installed on your machine and
available in your PATH. Instead, we load the results from a previous run of
ADMIXTURE.
If you would prefer a native clustering algorithm, we recommend using the
`gt_snmf` function, which is a wrapper for the `snmf` function from the `LEA`
package. sNMF is a fast clustering algorithm which provides results similar to
STRUCTURE and ADMIXTURE, and is available directly using the `tidypopgen`
package.
We can examine the suitability of our K values by plotting the cross-entropy
values for each K value, which is contained in the `cv` element of the
`gt_admix` object:

```{r, fig.alt = "Plot of cross-entropy for each value of K, showing K = 3 has the lowest cross-entropy"}
autoplot(anole_adm, type = "cv")
```

Here we can see that K = 3 is a sensible choice, as K = 3 represents the 'elbow' 
in the plot, where cross-entropy is at it's lowest. 

We can quickly plot this data with `autoplot` by using the type `barplot` and selecting 
our chosen value of `k`:

```{r, fig.alt = "Barplot of individuals coloured by predicted ancestry proportion (Q) from each of K ancestral sources"}
autoplot(anole_adm,
  k = 3, run = 1, data = anole_gt, annotate_group = FALSE,
  type = "barplot"
)
```

This plot is fine, but it is messy, and not a very helpful visualisation if we 
want to understand how our populations are structured.

To re-order this plot, grouping individuals by population, we can use the `annotate_group` 
and `arrange_by_group` arguments in autoplot:

```{r, fig.alt = "Barplot of individuals coloured by predicted ancestry proportion (Q) from each of K ancestral sources"}
autoplot(anole_adm,
  type = "barplot", k = 3, run = 1, data = anole_gt,
  annotate_group = TRUE, arrange_by_group = TRUE
)
```

This plot is much better. Now the plot is labelled by population we can see that
the individuals from each population are grouped together, with a few individuals
showing mixed ancestry between populations.

However, for a more visually appealing plot, we can re-order the individuals within 
each population as follows:

```{r, fig.alt = "Barplot of individuals coloured by predicted ancestry proportion (Q) from each of K ancestral sources, with individuals arranged according to their dominant ancestry propotion"}
autoplot(anole_adm,
  type = "barplot", k = 3, run = 1,
  data = anole_gt, annotate_group = TRUE, arrange_by_group = TRUE,
  arrange_by_indiv = TRUE, reorder_within_groups = TRUE
)
```

Now individuals are neatly ordered within each population.

For more complex/publication ready plots, we can extract the specific K value 
and run that we are interested in plotting, and add this .Q matrix to our 
gen_tibble object, so that we can create a custom plot with `ggplot2`. 

First we extract the q_matrix of interest using the `get_q_matrix` function:

```{r}
q_mat <- get_q_matrix(anole_adm, k = 3, run = 1)
```

Then we can easily add the data with the `augment` method:

```{r}
anole_gt_adm <- augment(q_mat, data = anole_gt)
head(anole_gt_adm)
```

Alternatively, we can convert our q matrix into `tidy` format, which is more 
suitable for plotting:

```{r}
tidy_q <- tidy(q_mat, anole_gt)
head(tidy_q)
```

And now we can use `ggplot2` directly to generate our custom plot:

```{r, fig.alt = "Barplot of individuals coloured by predicted ancestry proportion (Q) from each of K ancestral sources"}
tidy_q <- tidy_q %>%
  dplyr::group_by(id) %>%
  dplyr::mutate(dominant_q = max(percentage)) %>%
  dplyr::ungroup() %>%
  dplyr::arrange(group, dplyr::desc(dominant_q)) %>%
  dplyr::mutate(
    plot_order = dplyr::row_number(),
    id = factor(id, levels = unique(id))
  )

plt <- ggplot2::ggplot(tidy_q, ggplot2::aes(x = id, y = percentage, fill = q)) +
  ggplot2::geom_col(
    width = 1,
    position = ggplot2::position_stack(reverse = TRUE)
  ) +
  ggplot2::labs(
    y = "Population Structure for K = 3",
    title = "ADMIXTURE algorithm on A. punctatus"
  ) +
  theme_distruct() +
  scale_fill_distruct()

plt
```

In the Prates et al 2018 data, anolis lizards were assigned to three regions, 
described as Af, Eam, and Wam, acronyms which correspond to the Atlantic 
Forest, Eastern Amazonia, and Western Amazonia of Brazil. Our metadata also
contains this assignment, in the column `pop`. 

Lets say we wanted to change the grouping variable of our plot to match these
regions. We can use the `gt_admix_reorder_q` function to reorder the Q matrix by
a different grouping variable:

```{r}
anole_adm <- gt_admix_reorder_q(anole_adm, group = anole_gt$pop)
```

And replot the data:

```{r, fig.alt = "Barplot of individuals coloured by predicted ancestry proportion (Q) from each of K ancestral sources, labelled Atlantic forest or Amazonian forest"}
autoplot(anole_adm,
  type = "barplot", k = 3, run = 1,
  annotate_group = TRUE, arrange_by_group = TRUE,
  arrange_by_indiv = TRUE, reorder_within_groups = TRUE
)
```

And here we can see the clear distinction between the three regions, with a few individuals that have admixed ancestry.

# Handling Q matrices

For clustering algorithms that operate outside the R environment, 
the function `q_matrix()` can take a path to a directory containing results from multiple runs 
of a clustering algorithm for multiple values of K, read the .Q files, and summarise 
them in a single `q_matrix_list` object.

In the analysis above, through `gt_admxiture()`, we ran 1 repetition for K values 2 to 6. Let us
now collate the results from a standard run of ADMIXTURE for which we stored the files in
a directory:

```{r echo=FALSE, results='hide'}
# reload the admxiture results (they were reordered above)
anole_adm <- readRDS("a03_anole_adm.rds")
runs <- c(1)
k_values <- c(2:6)
q_matrices <- list()
adm_dir <- file.path(tempdir(), "anolis_adm")
if (!dir.exists(adm_dir)) {
  dir.create(adm_dir)
}

for (x in k_values) {
  q_matrices[[x]] <- list()

  for (i in runs) {
    q_matrices[[x]][[i]] <- get_q_matrix(anole_adm, k = x, run = i)

    write.table(q_matrices[[x]][[i]],
      file = paste0(adm_dir, "/K", x, "run", i, ".Q"),
      col.names = FALSE, row.names = FALSE, quote = FALSE
    )
  }
}
```

```{r}
adm_dir <- file.path(tempdir(), "anolis_adm")
list.files(adm_dir)
```

And read them back into our R environment using `q_matrix_list`:

```{r}
q_list <- read_q_files(adm_dir)
summary(q_list)
```

`q_matrix_list` has read and summarised the .Q files from our analysis, and we can 
access a single matrix from the list by selecting the run number and K value of interest 
using `get_q_matrix` as before.

For example, if we would like to view the second run of K = 3:

```{r}
head(get_q_matrix(q_list, k = 3, run = 1))
```

And, again, we can then autoplot any matrix by selecting from the
`q_matrix_list` object:

```{r, fig.alt = "Barplot of individuals coloured by predicted ancestry proportion (Q) from each of K ancestral sources"}
autoplot(get_q_matrix(q_list, k = 3, run = 1),
  data = anole_gt,
  annotate_group = TRUE, arrange_by_group = TRUE,
  arrange_by_indiv = TRUE, reorder_within_groups = TRUE
)
```

In this way, `tidypopgen` integrates with external clustering software
seamlessly for quick, easy plotting.
