Mapper Example Document

Run Mapper Algorithm

There are several clustering methods available, including DBSCAN, hierarchical clustering, k-means, and PAM. But you need to input all of the params required for the chosen method in method_params.

time_taken <- system.time({
  Mapper <- MapperAlgo(
    filter_values = data[,1:4],
    # filter_values = circle_data[,2:3],
    percent_overlap = 30,
    methods = "dbscan",
    method_params = list(eps = 1, minPts = 1),
    # methods = "hierarchical",
    # method_params = list(num_bins_when_clustering = 10, method = 'ward.D2'),
    # methods = "kmeans",
    # method_params = list(max_kmeans_clusters = 2),
    # methods = "pam",
    # method_params = list(num_clusters = 2),
    cover_type = 'stride',
    # intervals = 4,
    interval_width = 1,
    num_cores = 12
    )
})
time_taken

##    user  system elapsed 
##   0.078   0.035   1.225

Plots

There are built-in plotting functions to visualize the Mapper graph. You can choose between “ggraph” and “forceNetwork” types. Additionally, you can choose to average feature values over nodes or use conditional probability embeddings.

source('../R/Plotter.R')
MapperPlotter(Mapper, label=data$Species, data=data, type="forceNetwork", avg=FALSE, use_embedding=FALSE)

Also, you can create conditinoal probability embeddings

source('../R/CPEmbedding.R')

data$PW_group <- ifelse(data$Sepal.Width > 1.5, "wide", "narrow")
embedded <- CPEmbedding(Mapper, data, columns = list("PW_group", "Species"), a_level = "wide", b_level = "versicolor")

MapperPlotter(Mapper, label=embedded, data=data, type="forceNetwork", avg=TRUE, use_embedding=TRUE)

Correlation between Mapper graph and features

Sometimes it is useful to find out whether the Mapper graph structure correlates with certain features in the data. For example, if Sepal.Length densities are similar to Sepal.Width densities across the nodes in the Mapper graph.

source('../R/MapperCorrelation.R')

MapperCorrelation(Mapper, data = data, labels = list(data$Sepal.Length, data$Sepal.Width))

## `geom_smooth()` using formula = 'y ~ x'

Grid Search for optimal cover parameters

If you want to find optimal cover parameters for your data, you can use the GridSearch function. Observing the convergence of certain graph metrics as cover parameters change can help you select appropriate values.

source('../R/GridSearch.R')
cpe_params <- list("PW_group", "Species", "wide", "versicolor")
data$PW_group <- ifelse(data$Sepal.Width > 1.5, "wide", "narrow")
labels <- data%>%select(PW_group, Species)
GridSearch(
  filter_values = data[,1:4],
  label = labels,
  column = "Species",
  cover_type = "stride",
  width_vec = c(1),
  overlap_vec = c(30),
  num_cores = 12,
  out_dir = "../mapper_grid_outputs",
  avg = TRUE,
  use_embedding = cpe_params
)

## Cover=stride, Width=1.00, Overlap=30%
## Saved: ../mapper_grid_outputs/mapper_stride_w1.00_ov30.png , Elapsed: 1.472 sec