HAPPE: A Tool for Population Haplotype Analysis and Visualization in Editable Excel Tables
Haplotype identification, characterization and visualization are important for large-scale analysis and use in population genomics. Many tools have been developed to visualize haplotypes, but it is challenging to display both the pattern of haplotypes and the genotypes for each single SNP in the con...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-07-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.927407/full |
| _version_ | 1818241036399411200 |
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| author | Cong Feng Xingwei Wang Xingwei Wang Xingwei Wang Shishi Wu Shishi Wu Shishi Wu Weidong Ning Weidong Ning Bo Song Jianbin Yan Shifeng Cheng |
| author_facet | Cong Feng Xingwei Wang Xingwei Wang Xingwei Wang Shishi Wu Shishi Wu Shishi Wu Weidong Ning Weidong Ning Bo Song Jianbin Yan Shifeng Cheng |
| author_sort | Cong Feng |
| collection | DOAJ |
| description | Haplotype identification, characterization and visualization are important for large-scale analysis and use in population genomics. Many tools have been developed to visualize haplotypes, but it is challenging to display both the pattern of haplotypes and the genotypes for each single SNP in the context of a large amount of genomic data. Here, we describe the tool HAPPE, which uses the agglomerative hierarchical clustering algorithm to characterize and visualize the genotypes and haplotypes in a phylogenetic context. The tool displays the plots by coloring the cells and/or their borders in Excel tables for any given gene and genomic region of interest. HAPPE facilitates informative displays wherein data in plots are easy to read and access. It allows parallel display of several lines of values, such as phylogenetic trees, P values of GWAS, the entry of genes or SNPs, and the sequencing depth at each position. These features are informative for the detection of insertion/deletions or copy number variations. Overall, HAPPE provides editable plots consisting of cells in Excel tables, which are user-friendly to non-programmers. This pipeline is coded in Python and is available at https://github.com/fengcong3/HAPPE. |
| first_indexed | 2024-12-12T13:22:57Z |
| format | Article |
| id | doaj.art-47414a94c00344549eac510062233f7a |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-12T13:22:57Z |
| publishDate | 2022-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-47414a94c00344549eac510062233f7a2022-12-22T00:23:15ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-07-011310.3389/fpls.2022.927407927407HAPPE: A Tool for Population Haplotype Analysis and Visualization in Editable Excel TablesCong Feng0Xingwei Wang1Xingwei Wang2Xingwei Wang3Shishi Wu4Shishi Wu5Shishi Wu6Weidong Ning7Weidong Ning8Bo Song9Jianbin Yan10Shifeng Cheng11Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, ChinaGuangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, ChinaState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, ChinaShenzhen Research Institute of Henan University, Shenzhen, ChinaGuangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, ChinaState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, ChinaShenzhen Research Institute of Henan University, Shenzhen, ChinaGuangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, ChinaHubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, ChinaGuangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, ChinaGuangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, ChinaGuangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, ChinaHaplotype identification, characterization and visualization are important for large-scale analysis and use in population genomics. Many tools have been developed to visualize haplotypes, but it is challenging to display both the pattern of haplotypes and the genotypes for each single SNP in the context of a large amount of genomic data. Here, we describe the tool HAPPE, which uses the agglomerative hierarchical clustering algorithm to characterize and visualize the genotypes and haplotypes in a phylogenetic context. The tool displays the plots by coloring the cells and/or their borders in Excel tables for any given gene and genomic region of interest. HAPPE facilitates informative displays wherein data in plots are easy to read and access. It allows parallel display of several lines of values, such as phylogenetic trees, P values of GWAS, the entry of genes or SNPs, and the sequencing depth at each position. These features are informative for the detection of insertion/deletions or copy number variations. Overall, HAPPE provides editable plots consisting of cells in Excel tables, which are user-friendly to non-programmers. This pipeline is coded in Python and is available at https://github.com/fengcong3/HAPPE.https://www.frontiersin.org/articles/10.3389/fpls.2022.927407/fullhaplotypeSNPsphylogenetic clusteringvisualizationExcel |
| spellingShingle | Cong Feng Xingwei Wang Xingwei Wang Xingwei Wang Shishi Wu Shishi Wu Shishi Wu Weidong Ning Weidong Ning Bo Song Jianbin Yan Shifeng Cheng HAPPE: A Tool for Population Haplotype Analysis and Visualization in Editable Excel Tables Frontiers in Plant Science haplotype SNPs phylogenetic clustering visualization Excel |
| title | HAPPE: A Tool for Population Haplotype Analysis and Visualization in Editable Excel Tables |
| title_full | HAPPE: A Tool for Population Haplotype Analysis and Visualization in Editable Excel Tables |
| title_fullStr | HAPPE: A Tool for Population Haplotype Analysis and Visualization in Editable Excel Tables |
| title_full_unstemmed | HAPPE: A Tool for Population Haplotype Analysis and Visualization in Editable Excel Tables |
| title_short | HAPPE: A Tool for Population Haplotype Analysis and Visualization in Editable Excel Tables |
| title_sort | happe a tool for population haplotype analysis and visualization in editable excel tables |
| topic | haplotype SNPs phylogenetic clustering visualization Excel |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.927407/full |
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