20251213

.gitignore

@@ -14,3 +14,4 @@
 99.scripts/phyparts/
 .pueue.yml
 run.status
+!*/_description.md

00.rawdata/_description.md

@@ -7,4 +7,4 @@ This directory contains raw data used for analysis.
 - `clean_fastq` This folder contains cleaned FASTQ files after quality control.
 - `raw_fastq` This folder contains the original raw FASTQ files.
 - `sra` This folder contains SRA files downloaded from the NCBI database.
-- `sra.list` This file lists the SRA accession numbers for the datasets used in this project.
+- `sra.list` This file lists the SRA downloading links for the datasets used in this project.

99.scripts/workflow/phylogeny_reconstruction/03.snaq.jl

@@ -31,7 +31,7 @@ astraltree = readnewick(astralfile);
 
 ### Alternatively, reading in the input files from Bucky
 ### running in input_snaq/ folder
-inputCFfile = joinpath("..", "..", "input", "input.CFs.csv");
+inputCFfile = joinpath("bucky_1.CFs.csv");
 inputCF = readtableCF(inputCFfile);
 net0 = snaq!(astraltree, inputCF, hmax=0, filename="net0", seed=123, outgroup="Zju", runs=nruns);
 net1 = snaq!(net0, inputCF, hmax=1, filename="net1", seed=123, outgroup="Zju", runs=nruns);
@@ -60,7 +60,7 @@ rootatnode!(net4, "Zju");
 ### rotate!(net4, -2);
 
 ## Plotting the networks
-R"pdf"("snaq_networks.pdf", width=14, height=10);
+R"pdf"("snaq_networks_fulltree.pdf", width=14, height=10);
 R"layout(matrix(1:4, 2, 2, byrow=TRUE))"; # to get 4 plots into a single figure: 2 row, 2 columns
 R"par"(mar=[0, 0, 1.5, 0]);        # for smaller margins
 xmin, xmax = PhyloPlots.PhyloPlots.edgenode_coordinates(net1, false, false)[13:14];
@@ -81,9 +81,52 @@ plot(net4, showgamma=true, tipoffset=0.1, xlim=[xmin, xmax]);
 R"mtext"(string("hmax=4, loglik=-", round(loglik(net4), digits=2)), font=2);
 R"dev.off"();
 
+R"pdf"("snaq_networks_majortree.pdf", width=14, height=10);
+R"layout(matrix(1:4, 2, 2, byrow=TRUE))"; # to get 4 plots into a single figure: 2 row, 2 columns
+R"par"(mar=[0, 0, 1.5, 0]);        # for smaller margins
+xmin, xmax = PhyloPlots.PhyloPlots.edgenode_coordinates(net1, false, false)[13:14];
+xmax += (xmax - xmin) * 0.3;
+plot(net1, style=:majortree, showgamma=true, tipoffset=0.1, xlim=[xmin, xmax]);
+R"mtext"(string("hmax=1, loglik=-", round(loglik(net1), digits=2)), font=2);
+xmin, xmax = PhyloPlots.PhyloPlots.edgenode_coordinates(net2, false, false)[13:14];
+xmax += (xmax - xmin) * 0.3;
+plot(net2, style=:majortree, showgamma=true, tipoffset=0.1, xlim=[xmin, xmax]);
+R"mtext"(string("hmax=2, loglik=-", round(loglik(net2), digits=2)), font=2);
+xmin, xmax = PhyloPlots.PhyloPlots.edgenode_coordinates(net3, false, false)[13:14];
+xmax += (xmax - xmin) * 0.3;
+plot(net3, style=:majortree, showgamma=true, tipoffset=0.1, xlim=[xmin, xmax]);
+R"mtext"(string("hmax=3, loglik=-", round(loglik(net3), digits=2)), font=2);
+xmin, xmax = PhyloPlots.PhyloPlots.edgenode_coordinates(net4, false, false)[13:14];
+xmax += (xmax - xmin) * 0.3;
+plot(net4, style=:majortree, showgamma=true, tipoffset=0.1, xlim=[xmin, xmax]);
+R"mtext"(string("hmax=4, loglik=-", round(loglik(net4), digits=2)), font=2);
+R"dev.off"();
+
 ## expected vs. observed quartet concordance factors
-using CSV, DataFrames;
+using CSV, DataFrames, Distributions, Random, RCall;
+inputCFfile = joinpath("bucky_1.CFs.csv");
+inputCF = readtableCF(inputCFfile);
+net3 = readsnaqnetwork("net3.out");
+topologymaxQpseudolik!(net3, inputCF);
+df_long = fittedquartetCF(inputCF, :long);
+
+### Adding jitter to the points for better visualization
+Random.seed!(123);
+jitter = 0.005;
+df_jittered = deepcopy(df_long);
+df_jittered.obsCF .+= rand(Uniform(-jitter / 2, jitter / 2), nrow(df_long));
+df_jittered.expCF .+= rand(Uniform(-jitter / 2, jitter / 2), nrow(df_long));
+
+R"pdf"("expCFs_obsvsfitted.pdf", width=6, height=6);
+R"plot"(df_jittered.obsCF, df_jittered.expCF, xlab="quartet CF observed in gene trees",
+    ylab="quartet CF expected from network", pch=16,
+    col="#008080",
+    cex=0.7);
+R"abline"(0, 1, col="#008080", lwd=0.5);
+R"dev.off"();
 
 # Goodness of fit of the SNaQ networks
 using QuartetNetworkGoodnessFit;
+res1 = quarnetGoFtest!(net3, inputCF, true; seed=123, nsim=1000);
+res1[[1,2,3]] # p-value, uncorrected z, σ