Visualize Embeddings of Visits — visualize_visit

Visualize given embeddings of visits of specified specialties of doctors. The visualization is generated on the 2D plane by t-SNE algorithm or by PCA (two main components) and plotted with ggplot. If t-SNE cannot be generated (because for example perplexity is too large for the number of samples), there are plotted two main components from PCA. Points representing the visits can be colored by doctor ID, the first letter of ICD-10 code or by cluster number. The plot can be optionally saved to the given PDF file.

visualize_visit_embeddings(visits_vectors, visit_table, method = "tsne",
  color_by, spec = NULL, clusters, n_doctors = 5L, n_codes = 9L,
  save = FALSE, path_to_save)

Arguments

visit_table	A data frame with columns: `visit_id` `icd10` (Optional, if `color_by == "icd10"`): ICD-10 code of the visit `doctor_id` (Optional, if `color_by == "doctor"`): doctor's ID `specialties` Specialties of doctors, separated by `", "`
method	One of `"tsne"` (default) or `"pca"` - a method of generating the plot
color_by	A string, one of `{"doctor", "icd10", "cluster"}`
spec	A specialty to be plotted (optional, required if `color_by != "clusters"`)
clusters	An output of the function cluster_visits (optional, required if `color_by == "clusters"`)
n_doctors	A number of doctors to be colored, the rest will be grey (optional, required if `color_by == "doctor"`), default: 5
n_codes	A number of codes to be colored, the rest will be grey (optional, required if `color_by == "icd10"`), default: 9
save	A logical indicating if the plot should be saved to the file
path_to_save	An optional string of the path to the target PDF file
visit_vectors	A matrix of embeddings of visits

Value

A generated plot of embeddings.

Examples

inter_term_vectors <- embed_terms(interviews, embedding_size = 10L,
                                  term_count_min = 1L)
#> Error in .subset2(public_bind_env, "initialize")(...): unused arguments (word_vectors_size = 10, vocabulary = list(c("fever", "rhinitis", "cough", "eye", "thyroid"), c(3, 3, 4, 4, 6), c(3, 3, 4, 4, 6)))
exam_term_vectors <- embed_terms(examinations, embedding_size = 10L,
                                 term_count_min = 1L)
#> Error in .subset2(public_bind_env, "initialize")(...): unused arguments (word_vectors_size = 10, vocabulary = list(c("fever", "man", "mother", "cough", "heart", "patient", "thyroid", "eye", "rhinitis", "woman", "father"), c(2, 2, 2, 3, 3, 3, 3, 4, 5, 6, 7), c(2, 2, 2, 3, 3, 3, 3, 4, 5, 6, 7)))
visits_vectors <- embed_list_visits(interviews,
                                    examinations, inter_term_vectors,
                                    exam_term_vectors)
#> Error in ncol(term_vectors): object 'inter_term_vectors' not found

visualize_visit_embeddings(visits_vectors, visits, "tsne",
                           color_by = "doctor", spec = "internist", n_doctors = 10)
#> Error in visualize_visit_embeddings(visits_vectors, visits, "tsne", color_by = "doctor",     spec = "internist", n_doctors = 10): object 'visits_vectors' not found
visualize_visit_embeddings(visits_vectors, visits, "pca",
                           color_by = "doctor", spec = "internist", n_doctors = 9)
#> Error in visualize_visit_embeddings(visits_vectors, visits, "pca", color_by = "doctor",     spec = "internist", n_doctors = 9): object 'visits_vectors' not found
visualize_visit_embeddings(visits_vectors, visits,
                           color_by = "icd10", spec = "internist", n_codes = 4)
#> Error in visualize_visit_embeddings(visits_vectors, visits, color_by = "icd10",     spec = "internist", n_codes = 4): object 'visits_vectors' not found

clusters <- cluster_visits(visits_vectors, visits,
                           spec = "internist", cluster_number = 2)
#> Error in rownames(visits_vectors): object 'visits_vectors' not found
visualize_visit_embeddings(visits_vectors, visits,
                           color_by = "cluster",
                           clusters = clusters)
#> Error in visualize_visit_embeddings(visits_vectors, visits, color_by = "cluster",     clusters = clusters): object 'visits_vectors' not found