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add option to include additional mutation scores visualization (#13)
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* add -s option for scoresets vis

* fix dynamic link in readme

* fixed location issues

* fixed text alignment for score identifier

* changed plotting type for scores

* reformating and comments

* changed example data and output

* added score boundaries and scale

* handle empty vcfs

* warning if empty vcf header

---------

Co-authored-by: jonas-fuchs <[email protected]>
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PlushZ and jonas-fuchs authored May 22, 2024
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12 changes: 12 additions & 0 deletions README.md
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![Example](./example_data/example.png)

## SARS-CoV-2 example with additional score tracks `--scores`

![Example_Scores](./example_mave_data/example_scores.png)

## Installation

### via pip (recommened):
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restrict the plot to a specific genomic region.
--sort, --no-sort sort sample names alphanumerically (default: False)
--min-cov 20 display mutations covered at least x time (only if per base cov tsv files are provided)
-s scores_file pos_col score_col score_name, --scores scores_file pos_col score_col score_name
specify scores to be added to the plot by providing a CSV file containing scores, along with its column for amino-acid positions, its column for scores, and descriptive score names (e.g., expression, binding, antibody escape, etc.).
This option can be used multiple times to include multiple sets of scores.
-v, --version show program's version number and exit
```

You need to either provide the length of your reference genome or if you want to get the sequence annotation you will need to provide the gff3 file.

Additionally, you can also analyse if mutations are sufficiently covered and display non-covered cells in grey. For that first create a per base coverage tsv files for each bam file with [Qualimap](http://qualimap.conesalab.org/) and provide it in the same folder as the vcf files. Give them the same name as your vcf files.

Moreover, there is an option to include visualizations of additional scores (e.g., MAVE scores for binding affinity, expression level, antibody escape, etc.) mapped to mutations on the heatmap. To utilize this feature, use the -s or --scores
argument, and provide the following arguments: 1) path to the CSV file containing scores; 2) the name of the column in this file containing mutation positions in classic notation (e.g., T430Y); 3) the name of the column in this file containing the
scores themselves; 4) a descriptive score name that will be used as labels in the plot. Multiple score sets can be included simultaneously by repeating the -s or --scores option with different arguments. For example input and possible output data,
please refer to the files located in the [example_data/example_mave_data](example_mave_data) folder.

---

**Important disclaimer:**
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8,041 changes: 8,041 additions & 0 deletions example_mave_data/MaveBindRBD.csv
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8,041 changes: 8,041 additions & 0 deletions example_mave_data/MaveExpRBD.csv
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65 changes: 65 additions & 0 deletions example_mave_data/SARS-CoV-2.gff3
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##gff-version 3
#!gff-spec-version 1.21
#!processor NCBI annotwriter
##sequence-region NC_045512.2 1 29903
##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2697049
NC_045512.2 RefSeq region 1 29903 . + . ID=NC_045512.2:1..29903;Dbxref=taxon:2697049;collection-date=Dec-2019;country=China;gb-acronym=SARS-CoV-2;gbkey=Src;genome=genomic;isolate=Wuhan-Hu-1;mol_type=genomic RNA;nat-host=Homo sapiens;old-name=Wuhan seafood market pneumonia virus
NC_045512.2 RefSeq five_prime_UTR 1 265 . + . ID=id-NC_045512.2:1..265;gbkey=5'UTR
NC_045512.2 RefSeq gene 266 21555 . + . ID=gene-GU280_gp01;Dbxref=GeneID:43740578;Name=ORF1ab;gbkey=Gene;gene=ORF1ab;gene_biotype=protein_coding;locus_tag=GU280_gp01
NC_045512.2 RefSeq CDS 266 13468 . + 0 ID=cds-YP_009724389.1;Parent=gene-GU280_gp01;Dbxref=GenBank:YP_009724389.1,GeneID:43740578;Name=YP_009724389.1;Note=pp1ab%3B translated by -1 ribosomal frameshift;exception=ribosomal slippage;gbkey=CDS;gene=ORF1ab;locus_tag=GU280_gp01;product=ORF1ab polyprotein;protein_id=YP_009724389.1
NC_045512.2 RefSeq CDS 13468 21555 . + 0 ID=cds-YP_009724389.1;Parent=gene-GU280_gp01;Dbxref=GenBank:YP_009724389.1,GeneID:43740578;Name=YP_009724389.1;Note=pp1ab%3B translated by -1 ribosomal frameshift;exception=ribosomal slippage;gbkey=CDS;gene=ORF1ab;locus_tag=GU280_gp01;product=ORF1ab polyprotein;protein_id=YP_009724389.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 266 805 . + . ID=id-YP_009724389.1:1..180;Note=nsp1%3B produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=leader protein;protein_id=YP_009725297.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 806 2719 . + . ID=id-YP_009724389.1:181..818;Note=produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp2;protein_id=YP_009725298.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 2720 8554 . + . ID=id-YP_009724389.1:819..2763;Note=former nsp1%3B conserved domains are: N-terminal acidic (Ac)%2C predicted phosphoesterase%2C papain-like proteinase%2C Y-domain%2C transmembrane domain 1 (TM1)%2C adenosine diphosphate-ribose 1''-phosphatase (ADRP)%3B produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp3;protein_id=YP_009725299.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 8555 10054 . + . ID=id-YP_009724389.1:2764..3263;Note=nsp4B_TM%3B contains transmembrane domain 2 (TM2)%3B produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp4;protein_id=YP_009725300.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 10055 10972 . + . ID=id-YP_009724389.1:3264..3569;Note=nsp5A_3CLpro and nsp5B_3CLpro%3B main proteinase (Mpro)%3B mediates cleavages downstream of nsp4. 3D structure of the SARSr-CoV homolog has been determined (Yang et al.%2C 2003)%3B produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=3C-like proteinase;protein_id=YP_009725301.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 10973 11842 . + . ID=id-YP_009724389.1:3570..3859;Note=nsp6_TM%3B putative transmembrane domain%3B produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp6;protein_id=YP_009725302.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 11843 12091 . + . ID=id-YP_009724389.1:3860..3942;Note=produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp7;protein_id=YP_009725303.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 12092 12685 . + . ID=id-YP_009724389.1:3943..4140;Note=produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp8;protein_id=YP_009725304.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 12686 13024 . + . ID=id-YP_009724389.1:4141..4253;Note=ssRNA-binding protein%3B produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp9;protein_id=YP_009725305.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 13025 13441 . + . ID=id-YP_009724389.1:4254..4392;Note=nsp10_CysHis%3B formerly known as growth-factor-like protein (GFL)%3B produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp10;protein_id=YP_009725306.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 13442 13468 . + . ID=id-YP_009724389.1:4393..5324;Note=nsp12%3B NiRAN and RdRp%3B produced by pp1ab only;Parent=cds-YP_009724389.1;gbkey=Prot;product=RNA-dependent RNA polymerase;protein_id=YP_009725307.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 13468 16236 . + . ID=id-YP_009724389.1:4393..5324;Note=nsp12%3B NiRAN and RdRp%3B produced by pp1ab only;Parent=cds-YP_009724389.1;gbkey=Prot;product=RNA-dependent RNA polymerase;protein_id=YP_009725307.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 16237 18039 . + . ID=id-YP_009724389.1:5325..5925;Note=nsp13_ZBD%2C nsp13_TB%2C and nsp_HEL1core%3B zinc-binding domain (ZD)%2C NTPase/helicase domain (HEL)%2C RNA 5'-triphosphatase%3B produced by pp1ab only;Parent=cds-YP_009724389.1;gbkey=Prot;product=helicase;protein_id=YP_009725308.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 18040 19620 . + . ID=id-YP_009724389.1:5926..6452;Note=nsp14A2_ExoN and nsp14B_NMT%3B produced by pp1ab only;Parent=cds-YP_009724389.1;gbkey=Prot;product=3'-to-5' exonuclease;protein_id=YP_009725309.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 19621 20658 . + . ID=id-YP_009724389.1:6453..6798;Note=nsp15-A1 and nsp15B-NendoU%3B produced by pp1ab only;Parent=cds-YP_009724389.1;gbkey=Prot;product=endoRNAse;protein_id=YP_009725310.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 20659 21552 . + . ID=id-YP_009724389.1:6799..7096;Note=nsp16_OMT%3B 2'-o-MT%3B produced by pp1ab only;Parent=cds-YP_009724389.1;gbkey=Prot;product=2'-O-ribose methyltransferase;protein_id=YP_009725311.1
NC_045512.2 RefSeq CDS 266 13483 . + 0 ID=cds-YP_009725295.1;Parent=gene-GU280_gp01;Dbxref=GenBank:YP_009725295.1,GeneID:43740578;Name=YP_009725295.1;Note=pp1a;gbkey=CDS;gene=ORF1ab;locus_tag=GU280_gp01;product=ORF1a polyprotein;protein_id=YP_009725295.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 266 805 . + . ID=id-YP_009725295.1:1..180;Note=nsp1%3B produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=leader protein;protein_id=YP_009742608.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 806 2719 . + . ID=id-YP_009725295.1:181..818;Note=produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp2;protein_id=YP_009742609.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 2720 8554 . + . ID=id-YP_009725295.1:819..2763;Note=former nsp1%3B conserved domains are: N-terminal acidic (Ac)%2C predicted phosphoesterase%2C papain-like proteinase%2C Y-domain%2C transmembrane domain 1 (TM1)%2C adenosine diphosphate-ribose 1''-phosphatase (ADRP)%3B produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp3;protein_id=YP_009742610.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 8555 10054 . + . ID=id-YP_009725295.1:2764..3263;Note=nsp4B_TM%3B contains transmembrane domain 2 (TM2)%3B produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp4;protein_id=YP_009742611.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 10055 10972 . + . ID=id-YP_009725295.1:3264..3569;Note=nsp5A_3CLpro and nsp5B_3CLpro%3B main proteinase (Mpro)%3B mediates cleavages downstream of nsp4. 3D structure of the SARSr-CoV homolog has been determined (Yang et al.%2C 2003)%3B produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=3C-like proteinase;protein_id=YP_009742612.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 10973 11842 . + . ID=id-YP_009725295.1:3570..3859;Note=nsp6_TM%3B putative transmembrane domain%3B produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp6;protein_id=YP_009742613.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 11843 12091 . + . ID=id-YP_009725295.1:3860..3942;Note=produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp7;protein_id=YP_009742614.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 12092 12685 . + . ID=id-YP_009725295.1:3943..4140;Note=produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp8;protein_id=YP_009742615.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 12686 13024 . + . ID=id-YP_009725295.1:4141..4253;Note=ssRNA-binding protein%3B produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp9;protein_id=YP_009742616.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 13025 13441 . + . ID=id-YP_009725295.1:4254..4392;Note=nsp10_CysHis%3B formerly known as growth-factor-like protein (GFL)%3B produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp10;protein_id=YP_009742617.1
NC_045512.2 RefSeq mature_protein_region_of_CDS 13442 13480 . + . ID=id-YP_009725295.1:4393..4405;Note=produced by pp1a only;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp11;protein_id=YP_009725312.1
NC_045512.2 RefSeq stem_loop 13476 13503 . + . ID=id-GU280_gp01;Dbxref=GeneID:43740578;function=Coronavirus frameshifting stimulation element stem-loop 1;gbkey=stem_loop;gene=ORF1ab;inference=COORDINATES: profile:Rfam-release-14.1:RF00507%2CInfernal:1.1.2;locus_tag=GU280_gp01
NC_045512.2 RefSeq stem_loop 13488 13542 . + . ID=id-GU280_gp01-2;Dbxref=GeneID:43740578;function=Coronavirus frameshifting stimulation element stem-loop 2;gbkey=stem_loop;gene=ORF1ab;inference=COORDINATES: profile:Rfam-release-14.1:RF00507%2CInfernal:1.1.2;locus_tag=GU280_gp01
NC_045512.2 RefSeq gene 21563 25384 . + . ID=gene-GU280_gp02;Dbxref=GeneID:43740568;Name=S;gbkey=Gene;gene=S;gene_biotype=protein_coding;gene_synonym=spike glycoprotein;locus_tag=GU280_gp02
NC_045512.2 RefSeq CDS 21563 25384 . + 0 ID=cds-YP_009724390.1;Parent=gene-GU280_gp02;Dbxref=GenBank:YP_009724390.1,GeneID:43740568;Name=YP_009724390.1;Note=structural protein%3B spike protein;gbkey=CDS;gene=S;locus_tag=GU280_gp02;product=surface glycoprotein;protein_id=YP_009724390.1
NC_045512.2 RefSeq gene 25393 26220 . + . ID=gene-GU280_gp03;Dbxref=GeneID:43740569;Name=ORF3a;gbkey=Gene;gene=ORF3a;gene_biotype=protein_coding;locus_tag=GU280_gp03
NC_045512.2 RefSeq CDS 25393 26220 . + 0 ID=cds-YP_009724391.1;Parent=gene-GU280_gp03;Dbxref=GenBank:YP_009724391.1,GeneID:43740569;Name=YP_009724391.1;gbkey=CDS;gene=ORF3a;locus_tag=GU280_gp03;product=ORF3a protein;protein_id=YP_009724391.1
NC_045512.2 RefSeq gene 26245 26472 . + . ID=gene-GU280_gp04;Dbxref=GeneID:43740570;Name=E;gbkey=Gene;gene=E;gene_biotype=protein_coding;locus_tag=GU280_gp04
NC_045512.2 RefSeq CDS 26245 26472 . + 0 ID=cds-YP_009724392.1;Parent=gene-GU280_gp04;Dbxref=GenBank:YP_009724392.1,GeneID:43740570;Name=YP_009724392.1;Note=ORF4%3B structural protein%3B E protein;gbkey=CDS;gene=E;locus_tag=GU280_gp04;product=envelope protein;protein_id=YP_009724392.1
NC_045512.2 RefSeq gene 26523 27191 . + . ID=gene-GU280_gp05;Dbxref=GeneID:43740571;Name=M;gbkey=Gene;gene=M;gene_biotype=protein_coding;locus_tag=GU280_gp05
NC_045512.2 RefSeq CDS 26523 27191 . + 0 ID=cds-YP_009724393.1;Parent=gene-GU280_gp05;Dbxref=GenBank:YP_009724393.1,GeneID:43740571;Name=YP_009724393.1;Note=ORF5%3B structural protein;gbkey=CDS;gene=M;locus_tag=GU280_gp05;product=membrane glycoprotein;protein_id=YP_009724393.1
NC_045512.2 RefSeq gene 27202 27387 . + . ID=gene-GU280_gp06;Dbxref=GeneID:43740572;Name=ORF6;gbkey=Gene;gene=ORF6;gene_biotype=protein_coding;locus_tag=GU280_gp06
NC_045512.2 RefSeq CDS 27202 27387 . + 0 ID=cds-YP_009724394.1;Parent=gene-GU280_gp06;Dbxref=GenBank:YP_009724394.1,GeneID:43740572;Name=YP_009724394.1;gbkey=CDS;gene=ORF6;locus_tag=GU280_gp06;product=ORF6 protein;protein_id=YP_009724394.1
NC_045512.2 RefSeq gene 27394 27759 . + . ID=gene-GU280_gp07;Dbxref=GeneID:43740573;Name=ORF7a;gbkey=Gene;gene=ORF7a;gene_biotype=protein_coding;locus_tag=GU280_gp07
NC_045512.2 RefSeq CDS 27394 27759 . + 0 ID=cds-YP_009724395.1;Parent=gene-GU280_gp07;Dbxref=GenBank:YP_009724395.1,GeneID:43740573;Name=YP_009724395.1;gbkey=CDS;gene=ORF7a;locus_tag=GU280_gp07;product=ORF7a protein;protein_id=YP_009724395.1
NC_045512.2 RefSeq gene 27756 27887 . + . ID=gene-GU280_gp08;Dbxref=GeneID:43740574;Name=ORF7b;gbkey=Gene;gene=ORF7b;gene_biotype=protein_coding;locus_tag=GU280_gp08
NC_045512.2 RefSeq CDS 27756 27887 . + 0 ID=cds-YP_009725318.1;Parent=gene-GU280_gp08;Dbxref=GenBank:YP_009725318.1,GeneID:43740574;Name=YP_009725318.1;gbkey=CDS;gene=ORF7b;locus_tag=GU280_gp08;product=ORF7b;protein_id=YP_009725318.1
NC_045512.2 RefSeq gene 27894 28259 . + . ID=gene-GU280_gp09;Dbxref=GeneID:43740577;Name=ORF8;gbkey=Gene;gene=ORF8;gene_biotype=protein_coding;locus_tag=GU280_gp09
NC_045512.2 RefSeq CDS 27894 28259 . + 0 ID=cds-YP_009724396.1;Parent=gene-GU280_gp09;Dbxref=GenBank:YP_009724396.1,GeneID:43740577;Name=YP_009724396.1;gbkey=CDS;gene=ORF8;locus_tag=GU280_gp09;product=ORF8 protein;protein_id=YP_009724396.1
NC_045512.2 RefSeq gene 28274 29533 . + . ID=gene-GU280_gp10;Dbxref=GeneID:43740575;Name=N;gbkey=Gene;gene=N;gene_biotype=protein_coding;locus_tag=GU280_gp10
NC_045512.2 RefSeq CDS 28274 29533 . + 0 ID=cds-YP_009724397.2;Parent=gene-GU280_gp10;Dbxref=GenBank:YP_009724397.2,GeneID:43740575;Name=YP_009724397.2;Note=ORF9%3B structural protein;gbkey=CDS;gene=N;locus_tag=GU280_gp10;product=nucleocapsid phosphoprotein;protein_id=YP_009724397.2
NC_045512.2 RefSeq gene 29558 29674 . + . ID=gene-GU280_gp11;Dbxref=GeneID:43740576;Name=ORF10;gbkey=Gene;gene=ORF10;gene_biotype=protein_coding;locus_tag=GU280_gp11
NC_045512.2 RefSeq CDS 29558 29674 . + 0 ID=cds-YP_009725255.1;Parent=gene-GU280_gp11;Dbxref=GenBank:YP_009725255.1,GeneID:43740576;Name=YP_009725255.1;gbkey=CDS;gene=ORF10;locus_tag=GU280_gp11;product=ORF10 protein;protein_id=YP_009725255.1
NC_045512.2 RefSeq stem_loop 29609 29644 . + . ID=id-GU280_gp11;Dbxref=GeneID:43740576;function=Coronavirus 3' UTR pseudoknot stem-loop 1;gbkey=stem_loop;gene=ORF10;inference=COORDINATES: profile::Rfam-release-14.1:RF00165%2CInfernal:1.1.2;locus_tag=GU280_gp11
NC_045512.2 RefSeq stem_loop 29629 29657 . + . ID=id-GU280_gp11-2;Dbxref=GeneID:43740576;function=Coronavirus 3' UTR pseudoknot stem-loop 2;gbkey=stem_loop;gene=ORF10;inference=COORDINATES: profile::Rfam-release-14.1:RF00165%2CInfernal:1.1.2;locus_tag=GU280_gp11
NC_045512.2 RefSeq three_prime_UTR 29675 29903 . + . ID=id-NC_045512.2:29675..29903;gbkey=3'UTR
NC_045512.2 RefSeq stem_loop 29728 29768 . + . ID=id-NC_045512.2:29728..29768;Note=basepair exception: alignment to the Rfam model implies coordinates 29740:29758 form a noncanonical C:T basepair%2C but the homologous positions form a highly conserved C:G basepair in other viruses%2C including SARS (NC_004718.3);function=Coronavirus 3' stem-loop II-like motif (s2m);gbkey=stem_loop;inference=COORDINATES: profile:Rfam-release-14.1:RF00164%2CInfernal:1.1.2

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