add muller plots

.gitmodules

@@ -1,3 +1,6 @@
 [submodule "demon_model"]
 	path = resources/demon_model
 	url = https://github.com/robjohnnoble/demon_model
+[submodule "demonanalysis"]
+	path = resources/demonanalysis
+	url = https://github.com/robjohnnoble/demonanalysis

prepare-environments.sh

@@ -0,0 +1,36 @@
+###############################################################################
+#
+#   Create internal conda envs with all dependencies
+#
+#   AUTHOR: Maciej_Bak
+#   CONTACT: wsciekly.maciek@gmail.com
+#
+###############################################################################
+
+snakemake \
+    --snakefile="workflow/Snakefile" \
+    --configfile="tests/localtest/config-template.yml" \
+    --config workflow_repo_path="$PWD" \
+    --config workflow_analysis_outdir="$PWD/tests/localtest/output" \
+    --use-conda \
+    --conda-create-envs-only \
+    --cores 1 \
+    --nolock \
+    all
+
+for file in .snakemake/conda/*.yaml; do
+    if [ -f "$file" ]; then
+        if grep -q "name: warlock-r" "$file"; then
+            ENVPATH="${file%.yaml}"
+            break
+        fi
+    fi
+done
+
+eval "$(conda shell.bash hook)"
+conda deactivate
+conda activate $ENVPATH
+
+# strange error often appears, installation needs to be called twice
+Rscript -e "devtools::install('resources/demonanalysis', upgrade=TRUE)"
+Rscript -e "devtools::install('resources/demonanalysis', upgrade=TRUE)"

tests/localtest/config-template.yml

@@ -25,7 +25,7 @@ workflow_analysis_outdir: "{{ WORKFLOW_REPO_PATH }}/tests/localtest/output"
 ### DEMON PARAMETERS ###
 
 # spatial_structure
-demon_log2_deme_carrying_capacity: 8
+demon_log2_deme_carrying_capacity: [8, 9, 10]
 
 # dispersal
 demon_migration_type: 0
@@ -34,13 +34,13 @@ demon_migration_edge_only: 1
 demon_migration_rate_scales_with_K: 1
 
 # mutation_rates
-demon_mu_driver_birth: "1e-05"
-demon_mu_passenger: 0.001
-demon_mu_driver_migration: 0.01
+demon_mu_driver_birth: "5e-06"
+demon_mu_passenger: 0.1
+demon_mu_driver_migration: 0
 demon_passenger_pop_threshold: -1
 
 # fitness_effects
-demon_normal_birth_rate: [0.8, 0.9]
+demon_normal_birth_rate: 0.8
 demon_baseline_death_rate: 0
 demon_s_driver_birth: 0.1
 demon_s_passenger: 0
@@ -51,7 +51,7 @@ demon_max_relative_migration_rate: 10
 # non_biological_parameters
 demon_init_pop: 1
 demon_matrix_max: -1
-demon_max_pop: 1000000
+demon_max_pop: 100000
 demon_max_time: 86400
 demon_max_generations: 2000
 demon_seed: 10

warlock.sh

@@ -114,12 +114,17 @@ if [ -z "$CORES" ]; then
     CORES=1
 fi
 
+# in order to use R from conda-forge I need to set these env variables:
+LANG=en_US.UTF-8
+LC_ALL=en_US.UTF-8
+
 # select a proper smk profile based on the command line args
 case "$ENV" in
     local)
         snakemake \
             --configfile="$CONFIGFILE" \
             --profile="workflow/profiles/local" \
+            --use-conda \
             --cores="$CORES" \
             --nolock \
             all
@@ -128,6 +133,7 @@ case "$ENV" in
         snakemake \
             --configfile="$CONFIGFILE" \
             --profile="workflow/profiles/slurm" \
+            --use-conda \
             --cores="$CORES" \
             --nolock \
             all

workflow/Snakefile

@@ -166,7 +166,6 @@ rule run_demon:
         )
 
     params:
-        STR_runID = "{runID}",
         LOG_cluster_log = os.path.join(
             "{outdir}",
             "logs",
@@ -220,15 +219,90 @@ rule run_demon:
         """
 
 
+rule generate_summary_plots:
+    """
+    Generate per-simulation summary plots with 'demonanalysis' pkg.
+    """
+    input:
+        DIR_simulations_outdir = os.path.join(
+            "{outdir}",
+            "simulations",
+            "{runID}"
+        ),
+        SCRIPT_generate_summary_plots = os.path.join(
+            config["workflow_repo_path"],
+            "workflow",
+            "scripts",
+            "generate-summary-plots.R",
+        )
+
+    output:
+        DIR_analyses_outdir = directory(
+            os.path.join(
+                "{outdir}",
+                "analyses",
+                "{runID}"
+            )
+        )
+
+    params:
+        LOG_cluster_log = os.path.join(
+            "{outdir}",
+            "logs",
+            "{runID}",
+            "generate_summary_plots.cluster.log"
+        )
+
+    threads: 1
+
+    log:
+        LOG_local_stdout = os.path.join(
+            "{outdir}",
+            "logs",
+            "{runID}",
+            "generate_summary_plots.stdout.log"
+        ),
+        LOG_local_stderr = os.path.join(
+            "{outdir}",
+            "logs",
+            "{runID}",
+            "generate_summary_plots.stderr.log"
+        )
+
+    benchmark:
+        os.path.join(
+            "{outdir}",
+            "logs",
+            "{runID}",
+            "generate_summary_plots.benchmark.log"
+        )
+
+    conda:
+        "envs/warlock-r.yml"
+
+    shell:
+        """
+        (mkdir -p {output.DIR_analyses_outdir} \
+        && \
+        sleep 5 \
+        && \
+        Rscript {input.SCRIPT_generate_summary_plots} \
+        --input {input.DIR_simulations_outdir} \
+        --output {output.DIR_analyses_outdir}) \
+        1> {log.LOG_local_stdout} \
+        2> {log.LOG_local_stderr}
+        """
+
+
 rule all:
     """
     Target rule gathering final output of the workflow.
     """
     input:
-        DIR_simulations_outdir = expand(
+        DIR_analyses_outdir = expand(
             os.path.join(
                 "{outdir}",
-                "simulations",
+                "analyses",
                 "{runID}"
             ),
             outdir = config["workflow_analysis_outdir"],

workflow/envs/warlock-r.yml

@@ -0,0 +1,27 @@
+###############################################################################
+#
+#   AUTHOR: Maciej_Bak
+#   CONTACT: wsciekly.maciek@gmail.com
+#
+###############################################################################
+---
+
+  name: warlock-r
+
+  channels:
+    - conda-forge
+
+  dependencies:
+    - cmake=3.26.4
+    - compilers=1.3.0
+    - graphviz=2.50.0
+    - r-base=3.6.3
+    - r-devtools=2.4.1
+    - r-dplyr=1.0.6
+    - r-foreign=0.8_76
+    - r-ggplot2=3.3.3
+    - r-optparse=1.6.6
+    - r-readr=1.4.0
+    - r-rvaidememoire=0.9_79
+
+...

workflow/scripts/generate-summary-plots.R

@@ -0,0 +1,74 @@
+###############################################################################
+#
+#   Small wrapper to plot all Muller plots for warlock simulations.
+#
+#   AUTHOR: Maciek Bak
+#   AFFILIATION: City, University of London
+#   CONTACT: wsciekly.maciek@gmail.com
+#   CREATED: 23.11.2022
+#   LICENSE: Apache_2.0
+#
+###############################################################################
+
+Sys.setenv("LANGUAGE"="EN")
+
+# by default: suppress warnings
+options(warn = -1)
+
+# load libraries
+suppressPackageStartupMessages(suppressWarnings(library(demonanalysis)))
+suppressPackageStartupMessages(suppressWarnings(library(optparse)))
+
+# list the command-line arguments
+option_list <- list(
+  make_option(c("--input"),
+    action = "store_true",
+    dest = "input_directory",
+    type = "character",
+    help = "Path to the warlock output directory."
+  ),
+  make_option(c("--output"),
+    action = "store_true",
+    dest = "output_directory",
+    type = "character",
+    help = "Path for the output directory with plots."
+  ),
+  make_option(c("--help"),
+    action = "store_true",
+    dest = "help",
+    type = "logical",
+    default = FALSE,
+    help = "Show this information and exit."
+  ),
+  make_option(c("--verbose"),
+    action = "store_true",
+    dest = "verbose",
+    type = "logical",
+    default = FALSE,
+    help = "Run in verbose mode."
+  )
+)
+
+# parse command-line arguments
+opt_parser <- OptionParser(
+  usage = "Usage: %prog [OPTIONS] --message [STRING]",
+  option_list = option_list,
+  add_help_option = FALSE,
+  description = ""
+)
+opt <- parse_args(opt_parser)
+
+# if verbose flag was set: print warnings
+if (opt$verbose) {
+  options(warn = 0)
+}
+
+###############################################################################
+# MAIN
+###############################################################################
+
+plot_all_images(
+  path = opt$input_directory,
+  output_filename = "muller",
+  output_dir = opt$output_directory
+)