From 21337c56be7b2d66c2264f060f87291d4627786f Mon Sep 17 00:00:00 2001
From: jonathanspeh <jspeh@gmx.de>
Date: Thu, 25 Apr 2024 10:57:02 +0200
Subject: [PATCH] Added option to specify lambdas to simulator

---
 R/create_simulations.R                   | 22 +++++++++++++++-------
 man/simulate_sc.Rd                       |  5 ++++-
 tests/testthat/test-create_simulations.R |  8 ++++++++
 3 files changed, 27 insertions(+), 8 deletions(-)

diff --git a/R/create_simulations.R b/R/create_simulations.R
index 62ae88c..9e30f28 100644
--- a/R/create_simulations.R
+++ b/R/create_simulations.R
@@ -4,6 +4,7 @@
 #' @param n_cells_est estimated number of cells, will only be exact if multiple of six
 #' @param make_signature boolean weather to make a signature and write it to disk
 #' @param signature_path path for signature matrix
+#' @param lambdas either NULL for creating random lambdas or a numeric vector of length 6 to specify them
 #'
 #' @return a list containing the counts and annotaiton
 #' @export
@@ -12,7 +13,8 @@
 #' simulate_sc(n_genes = 100, n_cells_est = 30, make_signature = FALSE)
 
 simulate_sc <- function(n_genes = 10000, n_cells_est = 300,
-                        make_signature = TRUE, signature_path = "./signature.csv"){
+                        make_signature = TRUE, signature_path = "./signature.csv",
+                        lambdas = NULL){
   n1 <- round(n_cells_est/6)
   n2 <- round(n_cells_est/6)
   n3 <- round(n_cells_est/3)
@@ -22,13 +24,19 @@ simulate_sc <- function(n_genes = 10000, n_cells_est = 300,
 
   n_cells_actual <- n1 + n2 + n3 + n4 + n5 + n6
 
+    if(is.null(lambdas)){
+    lambdas <- sample(seq(0.01, 0.1, by = 0.01), 6, TRUE)
+  } else if(length(lambdas) != 6 | !is.numeric(lambdas)){
+      stop("lambdas must either be random or a numeric vector of length 6")
+  }
+
   counts <- Matrix::Matrix(cbind(
-    replicate(n1, rpois(n_genes, 0.01)),
-    replicate(n2, rpois(n_genes, 0.02)),
-    replicate(n3, rpois(n_genes, 0.06)),
-    replicate(n4, rpois(n_genes, 0.1)),
-    replicate(n5, rpois(n_genes, 0.05)),
-    replicate(n6, rpois(n_genes, 0.065))), sparse = TRUE)
+    replicate(n1, rpois(n_genes, lambdas[1])),
+    replicate(n2, rpois(n_genes, lambdas[2])),
+    replicate(n3, rpois(n_genes, lambdas[3])),
+    replicate(n4, rpois(n_genes, lambdas[4])),
+    replicate(n5, rpois(n_genes, lambdas[5])),
+    replicate(n6, rpois(n_genes, lambdas[6]))), sparse = TRUE)
 
   colnames(counts) <- paste0("cell_", rep(1:n_cells_actual))
   rownames(counts) <- paste0("gene_", rep(1:n_genes))
diff --git a/man/simulate_sc.Rd b/man/simulate_sc.Rd
index 6f6810e..5df15f2 100644
--- a/man/simulate_sc.Rd
+++ b/man/simulate_sc.Rd
@@ -8,7 +8,8 @@ simulate_sc(
   n_genes = 10000,
   n_cells_est = 300,
   make_signature = TRUE,
-  signature_path = "./signature.csv"
+  signature_path = "./signature.csv",
+  lambdas = NULL
 )
 }
 \arguments{
@@ -19,6 +20,8 @@ simulate_sc(
 \item{make_signature}{boolean weather to make a signature and write it to disk}
 
 \item{signature_path}{path for signature matrix}
+
+\item{lambdas}{either NULL for creating random lambdas or a numeric vector of length 6 to specify them}
 }
 \value{
 a list containing the counts and annotaiton
diff --git a/tests/testthat/test-create_simulations.R b/tests/testthat/test-create_simulations.R
index 6ad0455..5c57765 100644
--- a/tests/testthat/test-create_simulations.R
+++ b/tests/testthat/test-create_simulations.R
@@ -11,4 +11,12 @@ test_that("can simulated sc-set", {
   expect_equal(length(simulation), 2)
   expect_equal(dim(simulation$counts), c(n_genes, n_cells_est))
   expect_equal(dim(simulation$annotation), c(n_cells_est, 2))
+  expect_error(simulate_sc(n_genes = n_genes, n_cells_est = n_cells_est, make_signature = FALSE, lambdas = c(1,2,3)))
+  n_genes <- 100
+  n_cells_est <- 60
+  simulation <- simulate_sc(n_genes = n_genes, n_cells_est = n_cells_est, make_signature = FALSE, lambdas = c(1,2,3,4,5,6))
+  expect_equal(length(simulation), 2)
+  expect_equal(dim(simulation$counts), c(n_genes, n_cells_est))
+  expect_equal(dim(simulation$annotation), c(n_cells_est, 2))
+
   })