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changeset 24:ca6c19ee7da0 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d
author artbio
date Tue, 05 Jul 2022 21:41:43 +0000
parents 83f8c93c34b4
children b00fef2b1c2c
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/sig_contrib_table.tsv test-data/sig_contrib_table_v3.tsv test-data/sigmatrix.tab test-data/spectrum_output1.pdf test-data/user_output.pdf
diffstat 11 files changed, 63 insertions(+), 59 deletions(-) [+]
line wrap: on
line diff
--- a/mutational_patterns.R	Wed Oct 27 00:46:47 2021 +0000
+++ b/mutational_patterns.R	Tue Jul 05 21:41:43 2022 +0000
@@ -1,7 +1,8 @@
 # load packages that are provided in the conda env
-options(show.error.messages = F,
+options(show.error.messages = FALSE,
        error = function() {
-           cat(geterrmessage(), file = stderr()); q("no", 1, F)
+           cat(geterrmessage(), file = stderr())
+           q("no", 1, FALSE)
            }
         )
 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
@@ -202,16 +203,19 @@
     # (For larger datasets it is wise to perform more iterations by changing the nrun parameter
     # to achieve stability and avoid local minima)
     nmf_res <- extract_signatures(pseudo_mut_mat, rank = opt$newsignum, nrun = opt$nrun)
-    # Assign signature names
-    colnames(nmf_res$signatures) <- paste0("SBS", 1:opt$newsignum)
-    rownames(nmf_res$contribution) <- paste0("SBS", 1:opt$newsignum)
+    # Assign signature COSMICv3.2 names
+    cosmic_signatures <- get_known_signatures()
+    nmf_res <- rename_nmf_signatures(nmf_res, cosmic_signatures, cutoff = 0.85)
+    sim_matrix <- cos_sim_matrix(cosmic_signatures, nmf_res$signatures)
+    plot_cosine_sim <- plot_cosine_heatmap(sim_matrix)
+    grid.arrange(plot_cosine_sim)
     # Plot the 96-profile of the signatures:
     p5 <- plot_96_profile(nmf_res$signatures, condensed = TRUE)
     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 = T),
+    newcol <- paste0(gsub("\\..", "", new_sig_matrix$context, perl = TRUE),
                      "[", new_sig_matrix$substitution, "]",
-                     gsub("^.\\.", "", new_sig_matrix$context, perl = T))
+                     gsub("^.\\.", "", new_sig_matrix$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)
@@ -329,8 +333,8 @@
     fit_res <- fit_to_signatures(pseudo_mut_mat, sbs_signatures)
 
     # Plot contribution barplots
-    pc3 <- plot_contribution(fit_res$contribution, sbs_signatures, coord_flip = T, mode = "absolute")
-    pc4 <- plot_contribution(fit_res$contribution, sbs_signatures, coord_flip = T, mode = "relative")
+    pc3 <- plot_contribution(fit_res$contribution, sbs_signatures, coord_flip = TRUE, mode = "absolute")
+    pc4 <- plot_contribution(fit_res$contribution, sbs_signatures, coord_flip = TRUE, mode = "relative")
     if (is.na(opt$levels)[1]) {  # if there are NO levels to display in graphs
         pc3_data <- pc3$data
         pc3 <- ggplot(pc3_data, aes(x = Sample, y = Contribution, fill = as.factor(Signature))) +
@@ -397,7 +401,7 @@
                           level = rep("nolabels", length(fit_res_contrib[, 1])),
                           fit_res_contrib,
                           sum = rowSums(fit_res_contrib))
-        worklist <- worklist[order(worklist[, "sum"], decreasing = T), ]
+        worklist <- worklist[order(worklist[, "sum"], decreasing = TRUE), ]
         worklist <- worklist[1:opt$signum, ]
         worklist <- worklist[, -length(worklist[1, ])]
         worklist <- melt(worklist)
@@ -405,10 +409,10 @@
     } else {
         worklist <- list()
         for (i in levels(factor(levels_table$level))) {
-             fit_res$contribution[, levels_table$element_identifier[levels_table$level == i]] -> worklist[[i]]
+             worklist[[i]] <- fit_res$contribution[, levels_table$element_identifier[levels_table$level == i]]
              sum <- rowSums(as.data.frame(worklist[[i]]))
              worklist[[i]] <- cbind(worklist[[i]], sum)
-             worklist[[i]] <- worklist[[i]][order(worklist[[i]][, "sum"], decreasing = T), ]
+             worklist[[i]] <- worklist[[i]][order(worklist[[i]][, "sum"], decreasing = TRUE), ]
              worklist[[i]] <- worklist[[i]][1:opt$signum, ]
              worklist[[i]] <- worklist[[i]][, -length(as.data.frame(worklist[[i]]))]
         }
@@ -424,7 +428,7 @@
     p7 <-  ggplot(worklist, aes(x = "", y = value, group = signature, fill = signature)) +
               geom_bar(width = 1, stat = "identity") +
               geom_text(aes(label = label), position = position_stack(vjust = 0.5), color = "white", size = 3) +
-              coord_polar("y", start = 0) + facet_wrap(.~sample) +
+              coord_polar("y", start = 0) + facet_wrap(. ~ sample) +
               labs(x = "", y = "Samples", fill = tag) +
               scale_fill_manual(name = paste0(opt$signum, " most contributing\nsignatures\n(in each label/tissue)"),
                                 values = signature_colors[levels(worklist$signature)],
@@ -452,7 +456,7 @@
             output_table <- data.frame(sample = rownames(output_table), output_table)
             colnames(output_table) <- gsub("X", "SBS", colnames(output_table))
         }
-        write.table(output_table, file = opt$sig_contrib_matrix, sep = "\t", quote = F, row.names = F)
+        write.table(output_table, file = opt$sig_contrib_matrix, sep = "\t", quote = FALSE, row.names = FALSE)
     }
 
     # calculate all pairwise cosine similarities
--- a/mutational_patterns.xml	Wed Oct 27 00:46:47 2021 +0000
+++ b/mutational_patterns.xml	Tue Jul 05 21:41:43 2022 +0000
@@ -1,15 +1,15 @@
-<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy8">
+<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.4.0+galaxy0">
     <description>from genomic variations in vcf files</description>
     <requirements>
-        <requirement type="package" version="3.2.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement>
-        <requirement type="package" version="1.1.1l=h7f98852_0">openssl</requirement>
-        <requirement type="package" version="3.3.5=r41hc72bb7e_0">r-ggplot2</requirement>
-        <requirement type="package" version="1.6.6=r41hc72bb7e_1">r-optparse</requirement>
-        <requirement type="package" version="0.2.20=r41h03ef668_1002">r-rjson</requirement>
+        <requirement type="package" version="3.4.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement>
+        <!--requirement type="package" version="1.1.1l=h7f98852_0">openssl</requirement> -->
+        <requirement type="package" version="3.3.6=r41hc72bb7e_0">r-ggplot2</requirement>
+        <requirement type="package" version="1.7.1=r41hc72bb7e_0">r-optparse</requirement>
+        <requirement type="package" version="0.2.21=r41h7525677_1">r-rjson</requirement>
         <requirement type="package" version="0.21.0=r41h03ef668_1004">r-nmf</requirement>
         <requirement type="package" version="2.3=r41hc72bb7e_1003">r-gridextra</requirement>
-        <requirement type="package" version="1.4.3=r41hdfd78af_3">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement>
-        <requirement type="package" version="1.4.3=r41hdfd78af_3">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement>
+        <requirement type="package" version="1.4.3=r41hdfd78af_4">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement>
+        <requirement type="package" version="1.4.4=r41hdfd78af_0">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement>
 <!--
 install more bioconda genomes
 bioconductor-bsgenome.mmusculus.ucsc.mm9
@@ -200,6 +200,34 @@
 
     </outputs>
     <tests>
+         <!-- de novo signatures -->
+        <test>
+            <param name="vcfs">
+                <collection type="list">
+                    <element name="6" value="F.vcf"/>
+                    <element name="7" value="G.vcf"/>
+                    <element name="8" value="H.vcf"/>
+                    <element name="9" value="I.vcf"/>
+                </collection>
+            </param>
+            <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
+            <conditional name="set_spectrum">
+                <param name="choices" value="no"/>
+            </conditional>
+            <conditional name="set_denovo">
+                <param name="choices" value="yes"/>
+            </conditional>
+            <conditional name="set_preset">
+                <param name="choices" value="no"/>
+            </conditional>
+            <param name="nrun" value="10" />
+            <param name="rank" value="4" />
+            <param name="newsignum" value="4" />
+            <param name="rdata_out" value="true" />
+            <output name="denovo" file="denovo_output1.pdf" compare="sim_size"/>
+            <output name="sigmatrix" file="sigmatrix.tab" compare="sim_size"/>
+            <output name="rdata" file="denovo_1.RData" compare="sim_size" delta="400000"/> <!--  delta="170000" -->
+        </test>
          <!-- user defined (v3.2 restricted 30 minus 27 renamed to test nomenclature effect) -->
         <test>
             <param name="vcfs">
@@ -315,34 +343,6 @@
             </conditional>
             <output name="spectrum" file="spectrum_output1.pdf" compare="sim_size"/>
         </test>
-         <!-- de novo signatures -->
-        <test>
-            <param name="vcfs">
-                <collection type="list">
-                    <element name="6" value="F.vcf"/>
-                    <element name="7" value="G.vcf"/>
-                    <element name="8" value="H.vcf"/>
-                    <element name="9" value="I.vcf"/>
-                </collection>
-            </param>
-            <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
-            <conditional name="set_spectrum">
-                <param name="choices" value="no"/>
-            </conditional>
-            <conditional name="set_denovo">
-                <param name="choices" value="yes"/>
-            </conditional>
-            <conditional name="set_preset">
-                <param name="choices" value="no"/>
-            </conditional>
-            <param name="nrun" value="10" />
-            <param name="rank" value="4" />
-            <param name="newsignum" value="4" />
-            <param name="rdata_out" value="true" />
-            <output name="denovo" file="denovo_output1.pdf" compare="sim_size"/>
-            <output name="sigmatrix" file="sigmatrix.tab" compare="sim_size"/>
-            <output name="rdata" file="denovo_1.RData" compare="sim_size" delta="400000"/> <!--  delta="170000" -->
-        </test>
     </tests>
     <help>
 
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/sig_contrib_table.tsv	Wed Oct 27 00:46:47 2021 +0000
+++ b/test-data/sig_contrib_table.tsv	Tue Jul 05 21:41:43 2022 +0000
@@ -1,5 +1,5 @@
 sample	SBS1	SBS2	SBS3	SBS4	SBS5	SBS6	SBS7	SBS8	SBS9	SBS10	SBS11	SBS12	SBS13	SBS14	SBS15	SBS16	SBS17	SBS18	SBS19	SBS20	SBS21	SBS22	SBS23	SBS24	SBS25	SBS26	SBS27	SBS28	SBS29	SBS30
-ovary-I.vcf	0.107676737465178	0.0107477401085281	0.263118370815298	0	0.0975192598491968	0.00654300960428024	0	0.121325654310372	0.0675812234604709	0	0.0475946682228466	0.0483240788134274	0.00116766365611527	0	0.0195773794486755	0.128367970358363	0	0	0	0	0	0	0	0	0.0564468988265929	0	0.000297382010539655	0.0237119630501146	0	0
-ovary-H.vcf	0.105483533021363	0.0160722050763363	0.220294683323486	0	0.270646531625838	0	0	0.0632630764001629	0.0651960109780565	0	0.0265849338024135	0	0.00937728828228106	0	0	0.169077458531394	0	0	0	0	0	0	0	0	0.0141372418969508	0	0.0064233897483352	0.0334436473133834	0	0
-lung-G.vcf	0.210828794798222	0.0160042182355152	0.174216713183146	0	0.248848735805233	0	0	0.0079146795135654	0.122852241624819	0	0.0316731744534412	0.0400882001887818	0	0	0	0.0415901687752403	0	0	0.0349534584507835	0	0	0	0	0	0.0686079325155911	0	0.0013880107407027	0.00103367171495887	0	0
-lung-F.vcf	0.272200051777229	0.00523782090972898	0.176429226414213	0	0.107322684968036	0	0	0.0922420552015618	0.0176321903825532	0	0.0308049189266778	0.00421945577891649	0	0	0	0.195343895329217	0	0	0	0	0	0	0	0	0.026099693090191	0	0.0050497865751646	0.0410158172026456	0	0.0264024034438657
+6	0.272200051777229	0.00523782090972898	0.176429226414213	0	0.107322684968036	0	0	0.0922420552015618	0.0176321903825532	0	0.0308049189266778	0.00421945577891649	0	0	0	0.195343895329217	0	0	0	0	0	0	0	0	0.026099693090191	0	0.0050497865751646	0.0410158172026456	0	0.0264024034438657
+7	0.210828794798222	0.0160042182355152	0.174216713183146	0	0.248848735805233	0	0	0.0079146795135654	0.122852241624819	0	0.0316731744534412	0.0400882001887818	0	0	0	0.0415901687752403	0	0	0.0349534584507835	0	0	0	0	0	0.0686079325155911	0	0.0013880107407027	0.00103367171495887	0	0
+8	0.105483533021363	0.0160722050763363	0.220294683323486	0	0.270646531625838	0	0	0.0632630764001629	0.0651960109780565	0	0.0265849338024135	0	0.00937728828228106	0	0	0.169077458531394	0	0	0	0	0	0	0	0	0.0141372418969508	0	0.0064233897483352	0.0334436473133834	0	0
+9	0.107676737465178	0.0107477401085281	0.263118370815298	0	0.0975192598491968	0.00654300960428024	0	0.121325654310372	0.0675812234604709	0	0.0475946682228466	0.0483240788134274	0.00116766365611527	0	0.0195773794486755	0.128367970358363	0	0	0	0	0	0	0	0	0.0564468988265929	0	0.000297382010539655	0.0237119630501146	0	0
--- a/test-data/sig_contrib_table_v3.tsv	Wed Oct 27 00:46:47 2021 +0000
+++ b/test-data/sig_contrib_table_v3.tsv	Tue Jul 05 21:41:43 2022 +0000
@@ -1,5 +1,5 @@
 sample	SBS1	SBS2	SBS3	SBS4	SBS5	SBS6	SBS7a	SBS7b	SBS7c	SBS7d	SBS8	SBS9	SBS10a	SBS10b	SBS10c	SBS10d	SBS11	SBS12	SBS13	SBS14	SBS15	SBS16	SBS17a	SBS17b	SBS18	SBS19	SBS20	SBS21	SBS22	SBS23	SBS24	SBS25	SBS26	SBS27	SBS28	SBS29	SBS30	SBS31	SBS32	SBS33	SBS34	SBS35	SBS36	SBS37	SBS38	SBS39	SBS40	SBS41	SBS42	SBS43	SBS44	SBS45	SBS46	SBS47	SBS48	SBS49	SBS50	SBS51	SBS52	SBS53	SBS54	SBS55	SBS56	SBS57	SBS58	SBS59	SBS60	SBS84	SBS85	SBS86	SBS87	SBS88	SBS89	SBS90	SBS91	SBS92	SBS93	SBS94
-ovary-I.vcf	0.0248743382983054	0	0	0	0	0.0382804313784858	0.000279867877099847	0	0.0523368831013261	0	0.0882193437709409	0	0.00105713908429325	0	0	0	0	0	0.00790452113929918	0	0.0228952649764221	0.035824437322864	0	0	0.0157694785042366	0.00112106011995225	0	0.00901729432205061	0	0	0.0067314503274015	0.0424173427597118	0.00897709595233141	0	0.0134288190900345	0	0.0315118740824124	0.0274274413781644	0.0459722043929115	0.00919119609371442	0.0135875438956959	0	0	0.0813737079036436	0	0.134441510514793	0	0	0	0.00968535679523162	0.0232988957406608	0	0	0	0	0	0.00901138983347702	0.0232219272273402	0	0	0.0140535953847184	0	0	0.0588372989742489	0.126837942673735	0.000414033475201199	0	0	0	0	0.0123975208041955	0	0	0	0	0.00960179280510004	0	0
-ovary-H.vcf	0.0526112623195139	0	0	0.00259659019141931	0	0	0.00441492436160073	0	0.028442412784458	0.00371282908990969	0.0771150268514295	0	0.00469080414948085	0	0	0	0	0	0.0131075005010316	0	0	0.0564087542136608	0	0.00228775187171679	0	0.0197458393231762	0	0.00177238312166065	0	0	0.00886883514891954	0	0.00387092295756819	0.0034150231168899	0.0174808677883371	0	0.0435652656329046	0.001821180738257	0.0264091265962629	0.0107100101651646	0.0174453430547186	0	0	0.0961708355601418	0	0.121116601538177	0	0	0	0	0.0571796516660221	0	0	0	0	0.000214057521674493	0.0111211317159625	0.00829256700318903	0	0.00164798457109997	0.0258483341879308	0.00644458809280953	0	0.0846638702721653	0.122478370005574	0.00222471578608652	0	0.000420172000753205	0	0.00163043517541805	0.000141322538953654	0	0.0574873294316273	0.00242537895433406	0	0	0	0
-lung-G.vcf	0.0823617355865553	0	0	0	0	0.0525713539199432	0.00861488625601096	0	0.0339595873379564	0	0.0456255244916971	0.0145585252714382	0	0.000421381081383047	0	0	0	0	0.00522670784278192	0	0	0.0293382321445568	0.00139649570607906	0	0.0194196611974925	0.0386127956083362	0	0.013789732383022	0	0	0.0100733150661604	0.0349706130241875	0	0	0	0	0.0434093655847984	0.00181825891236839	0.0303474622606777	0	0.0187029901709085	0	0	0.120376065787024	0	0.0599280433448042	0	0	0.00132966985611013	0	0	0	0	0.0039271065334873	0	0	0	0.0280674592931216	0	0	0.035137879879521	0	0	0.0812463129866582	0.0917684488653737	0	0	0.0124734516843239	0	0.00901316909994899	0.00681265646517624	0	0.0647011123580966	0	0	0	0	0
-lung-F.vcf	0.125106083697333	0	0.0894527459328343	0	0	0	0	0	0.0324668080771622	0	0.0672874649502956	0	0.00268401866175131	0.00917023093306937	0	0	0	0	0	0	0	0.0451906045983062	0	0	0.00910592930802089	0.0167722110675364	0	0.0038298515888168	0	0	0.009531234514015	0	0	0	0.0232363343868912	0	0.062330351090351	0.00493364473237903	0.0324520312030243	0.00486738928923164	0.0100557162196348	0	0	0.0888476521405422	0	0.0556313157931215	0	0	0	0	0.020753584501296	0	0	0.0183541664469706	0	0.000330058861573153	0.00181335415290947	0.0123934694096205	0	0.00196180738612452	0.0392499133494657	0	0	0.0247940538178981	0.120319900452309	0.00358101555748017	0	0.0122742608109216	0.000420655172516775	0	0.0145849808127487	0	0.0316331756761206	0.00458398540772828	0	0	0	0
+6	0.125106083697333	0	0.0894527459328343	0	0	0	0	0	0.0324668080771622	0	0.0672874649502956	0	0.00268401866175131	0.00917023093306937	0	0	0	0	0	0	0	0.0451906045983062	0	0	0.00910592930802089	0.0167722110675364	0	0.0038298515888168	0	0	0.009531234514015	0	0	0	0.0232363343868912	0	0.062330351090351	0.00493364473237903	0.0324520312030243	0.00486738928923164	0.0100557162196348	0	0	0.0888476521405422	0	0.0556313157931215	0	0	0	0	0.020753584501296	0	0	0.0183541664469706	0	0.000330058861573153	0.00181335415290947	0.0123934694096205	0	0.00196180738612452	0.0392499133494657	0	0	0.0247940538178981	0.120319900452309	0.00358101555748017	0	0.0122742608109216	0.000420655172516775	0	0.0145849808127487	0	0.0316331756761206	0.00458398540772828	0	0	0	0
+7	0.0823617355865553	0	0	0	0	0.0525713539199432	0.00861488625601096	0	0.0339595873379564	0	0.0456255244916971	0.0145585252714382	0	0.000421381081383047	0	0	0	0	0.00522670784278192	0	0	0.0293382321445568	0.00139649570607906	0	0.0194196611974925	0.0386127956083362	0	0.013789732383022	0	0	0.0100733150661604	0.0349706130241875	0	0	0	0	0.0434093655847984	0.00181825891236839	0.0303474622606777	0	0.0187029901709085	0	0	0.120376065787024	0	0.0599280433448042	0	0	0.00132966985611013	0	0	0	0	0.0039271065334873	0	0	0	0.0280674592931216	0	0	0.035137879879521	0	0	0.0812463129866582	0.0917684488653737	0	0	0.0124734516843239	0	0.00901316909994899	0.00681265646517624	0	0.0647011123580966	0	0	0	0	0
+8	0.0526112623195139	0	0	0.00259659019141931	0	0	0.00441492436160073	0	0.028442412784458	0.00371282908990969	0.0771150268514295	0	0.00469080414948085	0	0	0	0	0	0.0131075005010316	0	0	0.0564087542136608	0	0.00228775187171679	0	0.0197458393231762	0	0.00177238312166065	0	0	0.00886883514891954	0	0.00387092295756819	0.0034150231168899	0.0174808677883371	0	0.0435652656329046	0.001821180738257	0.0264091265962629	0.0107100101651646	0.0174453430547186	0	0	0.0961708355601418	0	0.121116601538177	0	0	0	0	0.0571796516660221	0	0	0	0	0.000214057521674493	0.0111211317159625	0.00829256700318903	0	0.00164798457109997	0.0258483341879308	0.00644458809280953	0	0.0846638702721653	0.122478370005574	0.00222471578608652	0	0.000420172000753205	0	0.00163043517541805	0.000141322538953654	0	0.0574873294316273	0.00242537895433406	0	0	0	0
+9	0.0248743382983054	0	0	0	0	0.0382804313784858	0.000279867877099847	0	0.0523368831013261	0	0.0882193437709409	0	0.00105713908429325	0	0	0	0	0	0.00790452113929918	0	0.0228952649764221	0.035824437322864	0	0	0.0157694785042366	0.00112106011995225	0	0.00901729432205061	0	0	0.0067314503274015	0.0424173427597118	0.00897709595233141	0	0.0134288190900345	0	0.0315118740824124	0.0274274413781644	0.0459722043929115	0.00919119609371442	0.0135875438956959	0	0	0.0813737079036436	0	0.134441510514793	0	0	0	0.00968535679523162	0.0232988957406608	0	0	0	0	0	0.00901138983347702	0.0232219272273402	0	0	0.0140535953847184	0	0	0.0588372989742489	0.126837942673735	0.000414033475201199	0	0	0	0	0.0123975208041955	0	0	0	0	0.00960179280510004	0	0
--- a/test-data/sigmatrix.tab	Wed Oct 27 00:46:47 2021 +0000
+++ b/test-data/sigmatrix.tab	Tue Jul 05 21:41:43 2022 +0000
@@ -1,4 +1,4 @@
-Type	SBS1	SBS2	SBS3	SBS4
+Type	SBSA	SBSB	SBS5-like	SBSC
 A[C>A]A	2.537216e-02	2.002096e-02	1.710480e-02	2.141184e-02
 A[C>A]C	9.450873e-03	1.458332e-02	1.433290e-02	8.146530e-15
 A[C>A]G	2.154737e-06	2.245761e-03	7.951470e-03	3.165761e-03
Binary file test-data/spectrum_output1.pdf has changed
Binary file test-data/user_output.pdf has changed