changeset 25:b00fef2b1c2c draft

planemo upload for repository commit eeb46055822c6805c209af0c450ae941100960bd
author artbio
date Wed, 06 Jul 2022 11:43:09 +0000
parents ca6c19ee7da0
children af5c65ad5317
files mutational_patterns.R mutational_patterns.xml test-data/cosmic_output1.pdf test-data/cosmic_output_v3.pdf test-data/denovo_1.RData test-data/denovo_output1.pdf test-data/ test-data/spectrum_output1.pdf test-data/user_output.pdf
diffstat 9 files changed, 118 insertions(+), 109 deletions(-) [+]
line wrap: on
line diff
--- a/mutational_patterns.R	Tue Jul 05 21:41:43 2022 +0000
+++ b/mutational_patterns.R	Wed Jul 06 11:43:09 2022 +0000
@@ -70,6 +70,12 @@
     type = "integer",
     help = "Number of new signatures to be captured"
+    make_option(
+    "--cosmic_id_threshold",
+    default = 0.85,
+    type = "double",
+    help = "minimu cosine similarity to rename a new signature according to cosmic v3.2"
+  ),
     default = NA,
@@ -205,12 +211,14 @@
     nmf_res <- extract_signatures(pseudo_mut_mat, rank = opt$newsignum, nrun = opt$nrun)
     # Assign signature COSMICv3.2 names
     cosmic_signatures <- get_known_signatures()
-    nmf_res <- rename_nmf_signatures(nmf_res, cosmic_signatures, cutoff = 0.85)
+    nmf_res <- rename_nmf_signatures(nmf_res, cosmic_signatures, cutoff = opt$cosmic_id_threshold)
     sim_matrix <- cos_sim_matrix(cosmic_signatures, nmf_res$signatures)
     plot_cosine_sim <- plot_cosine_heatmap(sim_matrix)
     # Plot the 96-profile of the signatures:
     p5 <- plot_96_profile(nmf_res$signatures, condensed = TRUE)
+    grid.arrange(p5)
+    # write matrix of deno signatures for user
     new_sig_matrix <- reshape2::dcast(p5$data, substitution + context ~ sample, value.var = "freq")
     new_sig_matrix <- format(new_sig_matrix, scientific = TRUE)
     newcol <- paste0(gsub("\\..", "", new_sig_matrix$context, perl = TRUE),
@@ -218,7 +226,6 @@
                      gsub("^.\\.", "", new_sig_matrix$context, perl = TRUE))
     new_sig_matrix <- cbind(Type = newcol, new_sig_matrix[, seq_along(new_sig_matrix)[-c(1, 2)]])
     write.table(new_sig_matrix, file = opt$sigmatrix, quote = FALSE, row.names = FALSE, sep = "\t")
-    grid.arrange(p5)
     # Visualize the contribution of the signatures in a barplot
     pc1 <- plot_contribution(nmf_res$contribution, nmf_res$signature, mode = "relative", coord_flip = TRUE)
     # Visualize the contribution of the signatures in absolute number of mutations
@@ -231,18 +238,15 @@
     # The samples can be hierarchically clustered based on their euclidean dis- tance. The signatures
     # can be plotted in a user-specified order.
     # Plot signature contribution as a heatmap with sample clustering dendrogram and a specified signature order:
-    pch1 <- plot_contribution_heatmap(nmf_res$contribution,
-                                      sig_order = paste0("NewSig_", 1:opt$newsignum))
+    pch1 <- plot_contribution_heatmap(nmf_res$contribution, cluster_samples = TRUE)
     # Plot signature contribution as a heatmap without sample clustering:
     pch2 <- plot_contribution_heatmap(nmf_res$contribution, cluster_samples = FALSE)
     #Combine the plots into one figure:
     grid.arrange(pch1, pch2, ncol = 2, widths = c(2, 1.6))
     # Compare the reconstructed mutational profile with the original mutational profile:
-    plot_compare_profiles(pseudo_mut_mat[, 1],
-                          nmf_res$reconstructed[, 1],
-                          profile_names = c("Original", "Reconstructed"),
-                          condensed = TRUE)
+    pch3 <- plot_original_vs_reconstructed(pseudo_mut_mat, nmf_res$reconstructed, y_intercept = 0.95)
+    grid.arrange(pch3)
--- a/mutational_patterns.xml	Tue Jul 05 21:41:43 2022 +0000
+++ b/mutational_patterns.xml	Wed Jul 06 11:43:09 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.4.0+galaxy0">
+<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.4.0+galaxy1">
     <description>from genomic variations in vcf files</description>
         <requirement type="package" version="3.4.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement>
@@ -46,6 +46,7 @@
         --newsignum '$set_denovo.newsignum'
         --output_denovo '$denovo'
         --sigmatrix '$sigmatrix'
+        --cosmic_id_threshold '$set_denovo.cosmic_id_threshold'
     #end if
     #if $set_preset.choices == 'yes':
@@ -127,6 +128,9 @@
                 <param name="newsignum" type="integer" value="4" min="2" max="30"
                        label="Number of de novo signatures to capture"
                        help="High values extend the computational time. Note also that you cannot extract more signature than the number of available samples in the study"/>
+                <param name="cosmic_id_threshold" type="float" value="0.85" min="0" max="1"
+                       label="Minimum cosine similarity to rename a signature"
+                       help="If a signature has a cosine similarity higher than this value with a cosmic v3.2 signature, it will renamed accordingly, with a -like suffix"/>
             <when value="no" />
@@ -220,9 +224,10 @@
             <conditional name="set_preset">
                 <param name="choices" value="no"/>
-            <param name="nrun" value="10" />
+            <param name="nrun" value="30" />
             <param name="rank" value="4" />
-            <param name="newsignum" value="4" />
+            <param name="newsignum" value="2" />
+            <param name="cosmic_id_threshold" value="0.84" />
             <param name="rdata_out" value="true" />
             <output name="denovo" file="denovo_output1.pdf" compare="sim_size"/>
             <output name="sigmatrix" file="" compare="sim_size"/>
@@ -367,7 +372,7 @@
 * a collection of VCF files with somatic mutations calls from analysis of samples.
 * a tabular table describing the correspondance of sample names to levels of a factor
-(tissues, ages, sexes, etc.)
+  (tissues, ages, sexes, etc.)
Binary file test-data/cosmic_output1.pdf has changed
Binary file test-data/cosmic_output_v3.pdf has changed
Binary file test-data/denovo_1.RData has changed
Binary file test-data/denovo_output1.pdf has changed
--- a/test-data/	Tue Jul 05 21:41:43 2022 +0000
+++ b/test-data/	Wed Jul 06 11:43:09 2022 +0000
@@ -1,97 +1,97 @@
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+T[T>A]G	4.900357e-03	2.522573e-03
+T[T>A]T	2.439672e-02	1.853853e-02
+A[T>C]A	4.219870e-02	3.178417e-02
+A[T>C]C	7.399058e-03	9.255617e-03
+A[T>C]G	1.285954e-02	1.901398e-02
+A[T>C]T	1.290585e-02	1.296671e-02
+C[T>C]A	8.946937e-03	6.758427e-03
+C[T>C]C	1.097622e-02	8.213891e-03
+C[T>C]G	1.241063e-02	9.404346e-03
+C[T>C]T	1.587318e-02	1.467435e-02
+G[T>C]A	8.455188e-03	8.999783e-03
+G[T>C]C	2.931931e-03	6.618690e-03
+G[T>C]G	1.342277e-02	1.612988e-02
+G[T>C]T	1.283681e-02	6.674995e-03
+T[T>C]A	9.639435e-03	7.100539e-03
+T[T>C]C	1.361753e-02	1.815807e-02
+T[T>C]G	9.787002e-03	4.498450e-03
+T[T>C]T	3.444768e-02	2.723502e-02
+A[T>G]A	5.198391e-03	1.323929e-02
+A[T>G]C	4.405440e-04	3.062221e-03
+A[T>G]G	6.960889e-03	2.631345e-03
+A[T>G]T	3.082631e-03	6.448524e-03
+C[T>G]A	1.937101e-03	2.309071e-03
+C[T>G]C	3.886385e-03	4.826853e-04
+C[T>G]G	4.677149e-03	4.086015e-03
+C[T>G]T	4.583659e-03	2.130806e-03
+G[T>G]A	2.808671e-03	1.699607e-03
+G[T>G]C	1.950620e-03	3.043178e-03
+G[T>G]G	9.744602e-03	8.480532e-03
+G[T>G]T	8.646393e-03	8.409194e-03
+T[T>G]A	5.149241e-03	3.178257e-03
+T[T>G]C	4.318309e-03	5.427921e-03
+T[T>G]G	1.461769e-02	7.848913e-03
+T[T>G]T	2.902799e-02	2.042809e-02
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