Merge pull request #102 from SpatialHackathon/metric_lisi_kbiharie

Metric LISI Score

metric/LISI/LISI.r

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+#!/usr/bin/env Rscript
+
+# Author_and_contribution: Niklas Mueller-Boetticher; created template
+# Author_and_contribution: Kirti Biharie; implemented LISI score
+
+suppressPackageStartupMessages(library(optparse))
+
+option_list <- list(
+  make_option(
+    c("-l", "--labels"),
+    type = "character", default = NULL,
+    help = "Labels from domain clustering."
+  ),
+  make_option(
+    c("-g", "--ground_truth"),
+    type = "character", default = NA,
+    help = "Groundtruth labels."
+  ),
+  make_option(
+    c("-e", "--embedding"),
+    type = "character", default = NA,
+    help = "Embedding of points in latent space. Potential usage for metrics without groundtruth."
+  ),
+  # format should be json
+  make_option(
+    c("-c", "--config"),
+    type = "character", default = NA,
+    help = "Optional config file (json) used to pass additional parameters."
+  ),
+  make_option(
+    c("-o", "--out_file"),
+    type = "character", default = NULL,
+    help = "Output file."
+  )
+)
+
+description <- "Calculate LISI Score"
+
+opt_parser <- OptionParser(
+  usage = description,
+  option_list = option_list
+)
+opt <- parse_args(opt_parser)
+
+# Use these filepaths as input
+label_file <- opt$labels
+
+if (!is.na(opt$ground_truth)) {
+  groundtruth_file <- opt$ground_truth
+}
+if (!is.na(opt$embedding)) {
+  embedding_file <- opt$embedding
+}
+if (!is.na(opt$config)) {
+  config_file <- opt$config
+}
+
+
+## Your code goes here
+library(lisi)
+library(rjson)
+
+if (is.na(opt$ground_truth)) {
+  stop("Groundtruth labels needed to calculate the LISI Score")
+}
+
+if (is.na(opt$embedding)) {
+  stop("Embeddings needed to calculate the LISI Score")
+}
+
+if (is.na(opt$config)) {
+  stop("Config file not provided")
+}
+
+ground_truth <- read.delim(groundtruth_file, sep="\t", row.names=1)
+embeddings <- read.delim(embedding_file, sep="\t", row.names=1)
+config <- fromJSON(file=config_file)
+
+common_index <- intersect(rownames(ground_truth), rownames(embeddings))
+ground_truth <- ground_truth[common_index,,drop=FALSE]
+embeddings <- embeddings[common_index,,drop=FALSE]
+
+metric <- mean(compute_lisi(embeddings, ground_truth, "label", perplexity=config$perplexity)[,"label"])
+
+## Write output
+outfile <- file(opt$out_file)
+dir.create(dirname(opt$out_file), showWarnings = FALSE, recursive = TRUE)
+
+writeLines(format(metric, digits = 6, scientific = TRUE), outfile)
+close(outfile)

metric/LISI/LISI.yml

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+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - r-base=4.3.1
+  - r-optparse=1.7.3
+  - r-lisi=1.0
+  - r-rjson=0.2.21

metric/LISI/config/config_1.json

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+{"perplexity": 15}