CN113946324A - Interactive visual report system for displaying high-throughput sequencing data result - Google Patents
Interactive visual report system for displaying high-throughput sequencing data result Download PDFInfo
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- CN113946324A CN113946324A CN202111060102.9A CN202111060102A CN113946324A CN 113946324 A CN113946324 A CN 113946324A CN 202111060102 A CN202111060102 A CN 202111060102A CN 113946324 A CN113946324 A CN 113946324A
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- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06F—ELECTRIC DIGITAL DATA PROCESSING
- G06F8/00—Arrangements for software engineering
- G06F8/30—Creation or generation of source code
- G06F8/34—Graphical or visual programming
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- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06F—ELECTRIC DIGITAL DATA PROCESSING
- G06F8/00—Arrangements for software engineering
- G06F8/30—Creation or generation of source code
- G06F8/38—Creation or generation of source code for implementing user interfaces
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- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06F—ELECTRIC DIGITAL DATA PROCESSING
- G06F9/00—Arrangements for program control, e.g. control units
- G06F9/06—Arrangements for program control, e.g. control units using stored programs, i.e. using an internal store of processing equipment to receive or retain programs
- G06F9/44—Arrangements for executing specific programs
- G06F9/445—Program loading or initiating
- G06F9/44521—Dynamic linking or loading; Link editing at or after load time, e.g. Java class loading
- G06F9/44526—Plug-ins; Add-ons
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B45/00—ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
Abstract
The invention provides an interactive visual report system for displaying high-throughput sequencing data results, which comprises a report generating and connecting module, a plug-in module, a report template editing module and a management module, wherein the report generating and connecting module is used for generating a report; the report generation and connection module is used for connecting a Markdown report template, multigroup mathematical data, plug-ins and other files and converting the report template into an online HTML report; the plug-in module is used for realizing dynamic loading and compiling of plug-ins; the report template editing module is used for online writing and debugging of the report template; the management module is used for tracing and managing the report template writing process and the generation process. Compared with the prior art, the system can calculate and generate the dynamic graph in real time, and has strong interactive operation capability, high customization and community sharing.
Description
Technical Field
The invention relates to the technical field of computers, in particular to an interactive visual report system for displaying a high-throughput sequencing data result.
Background
With the progress of high throughput detection technology, the genetic background, gene transcription, protein expression and metabolism of the body can be deeply understood by detecting various substances such as DNA, RNA, protein, metabolites, etc., and the generated Data such as genome (Genomics), transcriptome (Transcriptomics), proteome (Proteomics), metabolome (Metabolomics) and the like are collectively called multigenomic Data (Multi-Omics Data). The clinical application of the multiomic data provides ideas and methods for etiology exploration, guides the direction of disease prevention, diagnosis and treatment and becomes an important component in precise medicine. By analyzing multiple groups of chemical data and generating corresponding analysis reports, the method is a direct entrance for refining knowledge of users and determines the accuracy and consistency of result information finally accepted by the users.
However, in the conventional static report, the static chart is usually difficult to modify once generated by calculation, and if a new index combination is required to be added, the chart needs to be regenerated and the static report needs to be sorted, so that the difficulties in managing, tracing and multiplexing the report and the chart are high. In addition, most static charts are selectively displayed, report results are separated from the charts and cannot be interacted, and real data are difficult to directly observe. This not only violates the "precision" concept of precision medicine, but also can cause serious impact on the development and application of precision medicine.
Disclosure of Invention
The present invention is directed to overcoming the above-mentioned drawbacks of the prior art, and providing an interactive visual reporting system for displaying the result of high throughput sequencing data, which can calculate and generate a dynamic graph in real time, and has a strong interactive operation capability, a highly customizable and community sharing mode.
The purpose of the invention can be realized by the following technical scheme:
an interactive visual reporting system for displaying high throughput sequencing data results, comprising:
the report generation and connection module is used for connecting the Markdown report template, the multiple groups of mathematical data and the plug-in units and converting the report template into an online HTML report;
the report template editing module is used for performing online writing and debugging on the report template;
the plug-in module is used for realizing the dynamic loading and compiling of the plug-ins and providing corresponding plug-ins for the report template editing module;
and the management module is used for managing the traceable operation of the report template writing process and the generation process.
Further, the report generation and connection module includes:
the plug-in grammar unit is used for generating custom plug-in grammar;
the Markdown interpreter calls the corresponding plug-in by identifying the self-defined plug-in grammar, transmits related parameters and data, and embeds a JavaScript code generated after the plug-in runs into a Markdown template in the form of a script tag; and according to a self-defined analysis rule, converting the related parameters and the data and finishing the rendering of Markdown and the generation of a report.
Further, the customized parsing rules comprise lexical parsing rules, grammar parsing rules and code generation/execution rules. The parsing execution of the customized parsing rule comprises the following steps:
1) lexical analysis: recognizing the character string as a word sequence according to a word forming rule;
2) and (3) syntax analysis: combining the word sequences into phrases;
3) code generation/execution: and searching a corresponding plug-in according to the phrase, transmitting the parameter list obtained by analysis, initializing a plug-in class, processing the parameter list, caching all data files to a specified working directory, replacing a file path, calling a run method in a plug-in example to generate a JavaScript code related to a visual chart, and inserting the JavaScript code into a Markdown file specified position by a script tag.
Further, the self-defined plug-in grammar is a conventional grammar following function calling in a general language, the self-defined plug-in grammar comprises plug-ins and a parameter list, the plug-ins are provided with special characters, and the special characters and plug-in names form identifiers.
Further, the card module includes:
the plug-in dynamic loading unit is used for identifying the plug-ins meeting the requirements in the current environment and registering the plug-ins into a plug-in list for calling when a report is generated subsequently;
the interactive plug-in library stores various plug-ins of the plug-ins. Further, the interactive plug-in library stores plug-ins including table type plug-ins, perspective and perspective table type plug-ins and interactive visual graph plug-ins. Further, the interactive visualization graph plug-in dynamically generates a dynamic chart for displaying report results by adopting a self-defined parameter control panel and a real-time calculation mode.
Further, the report template editing module comprises:
the Web service unit is used for providing functions of downloading user registration channel data, modifying and rendering report files in real time, interactively displaying the report files and the like;
the Markdown editor executes online editing, debugging and previewing of the Markdown text through the Web service unit;
and the file monitoring unit is used for judging whether the file is modified or not by monitoring the change of the report file in the specified directory.
Further, the management module includes:
the report template sample generation tool provides a corresponding report template generation command for a user to generate a report template sample which accords with the best practice specification and a corresponding description document;
the report template version control is realized, and the version control of the report template is realized;
and the plug-in and plug-in library management unit is used for managing the interactive plug-in library and the plug-ins, and the plug-ins also comprise various visual plug-ins developed by the community and visual plug-ins of specified versions installed in the online plug-in warehouse by one key.
Compared with the prior art, the invention has the following advantages:
1) highly customizable. According to the invention, the self-defined plug-in grammar is generated through the plug-in grammar unit, the corresponding plug-in is flexibly called by using the Markdown interpreter, and the JavaScript code generated after the plug-in is operated is embedded into the Markdown template in the form of a script tag, so that compared with a static chart, the efficient interaction can be realized, and the high-efficiency customizable report generation function can be realized.
2) And calculating and generating a dynamic graph in real time. According to the invention, by loading the interactive visual chart plug-in, a dynamic chart is dynamically generated by adopting a self-defined parameter control panel and a real-time calculation mode, and real-time, dynamic and multi-dimensional display and report result exploration can be realized.
3) Has strong interactive operation capability. According to the invention, through setting the interactive plug-in library, plug-in types are various, abundant visual charts are provided, and the analysis results of multigroup mathematical data can be comprehensively displayed.
4) And (4) community sharing. According to the invention, the plug-in meeting the Entry Point requirement in the current environment is automatically identified through the plug-in dynamic loading unit, and the dynamically loaded plug-in is added into the report system, so that the sharing and multiplexing of the report are realized.
Drawings
FIG. 1 is a schematic diagram illustrating an interactive visual reporting system for displaying results of high throughput sequencing data according to an embodiment of the present invention;
FIG. 2 is a diagram of plug-in call syntax and visualization;
FIG. 3 is a conventional pattern of results;
fig. 4 shows a mode of an interactive visual reporting system for displaying the result of high throughput test data according to the embodiment.
Detailed Description
The invention is described in detail below with reference to the figures and specific embodiments. The present embodiment is implemented on the premise of the technical solution of the present invention, and a detailed implementation manner and a specific operation process are given, but the protection scope of the present invention is not limited to the following embodiments.
Referring to fig. 1, the present embodiment provides an interactive visual reporting system for displaying the result of high throughput sequencing data, comprising: the report template generation and connection module M1, the plug-in module M2, the report template editing module M3 and the management module M4.
Report template generation and connection module M1: the system is used for connecting a Markdown report template, a plurality of groups of mathematical data, plug-ins and other files required by a report to be generated, and converting the report template into an online HTML report;
the report module generation and connection module M1 includes a plug-in grammar unit 11 and a Markdown interpreter 12, and completes conversion of the content of the Markdown report template into a visual plug-in calling grammar, and then generates a visual chart code by recognizing the corresponding grammar, and finally completes generation of the Markdown report.
The plug-in grammar unit 11 is used for generating a self-defined plug-in grammar and appointing a plug-in and parameters and a data path required by the operation of the plug-in a Markdown report template;
the self-defined plug-in grammar follows the function calling common grammar in the common language, consists of a plug-in and a parameter list, introduces @ as a special character, and consists of @ and a plug-in name together to form an identifier;
the Markdown interpreter 12 is mainly developed based on a Python pymatching package, identifies corresponding grammar through an identifier, analyzes the grammar into a plug-in name and parameter list according to a self-defined grammar analysis rule, calls corresponding plug-ins through a plug-in system, transmits related parameters and data, and embeds JavaScript codes generated after the plug-ins operate into a Markdown template in the form of script tags; the input of a user is converted into a series of code blocks consisting of JavaScript, HTML and CSS codes and embedded into the report, and the rendering of Markdown and the generation of the report are completed, so that the problem of report traceability caused by separation of report content and chart generation is solved.
The parsing execution of the Markdown interpreter 12 comprises the following steps:
101) lexical analysis: recognizing a long string of character strings which are connected in a whole line or a plurality of lines of character strings into a word sequence according to a word forming rule defined in advance;
102) and (3) syntax analysis: combining word sequences into phrases on the basis of lexical analysis, and judging whether the structure of the phrases accords with the predefined specification;
103) code generation/execution: based on the grammar phrase obtained by grammar analysis, a corresponding plug-in is searched from a plug-in registry, a parameter list obtained by analysis is introduced, a plug-in class is initialized, then a parameter preprocessor is called to process the parameter list, all data files are cached to a designated working directory, a file path is replaced, a run method in a plug-in instance is called to generate a JavaScript code related to a visual chart, and the JavaScript code is inserted into a Markdown file designated position by a script tag.
Plug-in module M2: the dynamic loading and compiling of the plug-in are realized;
the plug-in module M2 comprises a plug-in dynamic loading unit 21 and an interactive plug-in library 22;
the plug-in module M2 also comprises a set of plug-in development specifications, and the plug-in development specifications are used for stipulating the preparation work of a plug-in developer for generating plug-ins which can be called by a plug-in system based on a specific language specification;
the plug-in dynamic loading unit 21 is implemented based on an Entry Point mechanism of a Python package, and is used for identifying a plug-in meeting requirements in the current environment, and registering the plug-in to a plug-in list for calling when a report is subsequently generated;
and constructing subclasses of specific plug-ins based on a BasePlugin base class, wherein the subclasses are mainly responsible for completing operations such as preparation of data files and generation of visual codes, and meanwhile, defining a clear Entry Point in a Python package management file.
The interactive plug-in library 22 is used for storing various types of plug-ins, including table type plug-ins, perspective and perspective table type plug-ins and interactive visual diagram plug-ins;
the interactive visual graph plug-in dynamically generates a dynamic graph by adopting a user-defined parameter control panel and a real-time calculation mode, and can realize dynamic and multi-dimensional display and explore report results.
Fig. 3 and 4 show a comparison of a conventional result presentation mode and an interactive visual reporting system presentation mode.
In particular, researchers have presented and published data results in static charts, and data, code, and computing environments associated with static charts may not be shared therewith according to specifications, at which point other researchers may face the problem of difficulty in repeating static charts and the inability to explore the data further. In the interactive visual report system mode, researchers publish reports as online display websites based on Markdown, data and interactive plug-ins, and other researchers can perform dynamic interactive click on interested charts at webpage ends to check data distribution characteristics of different index combinations.
The mode of the interactive visual report system provided by the embodiment is significantly superior to that of a static chart, not only can a chart in research be reproduced, but also multiple persons can be supported to simultaneously operate and explore research data, the distribution characteristics of indexes in the data can be displayed according to requirements, the interactive visual report system is not limited to indexes published with articles, and the interactive visual report system is more beneficial to realizing two goals of effective management and traceability and reusability of reports.
Report template editing module M3: online composition and debugging of report templates;
the report template editing module M3 includes a Markdown editor 31, a Web service unit 32 and a file monitoring unit 33,
the Markdown editor 31 is developed by Javascript and used for editing and previewing Markdown texts;
the Web service unit 32 is developed by adopting a Python Web framework Tornado; and functions of downloading data of a user registration channel, modifying and rendering report files in real time, interactively displaying the report files and the like are provided.
The file monitoring unit 33 is developed by Python and is used for judging whether the file is modified or not by monitoring the file change in the specified directory.
The management module M4: traceability operations and management for the report template composition process and generation process.
The management module M4 includes: a report template sample generation tool 41, a report template version control 42, and a plug-in and plug-in library management unit 43.
The report template sample generating tool 41 is based on the Python Jinja2 template language, and a user provides a corresponding report template generating command to generate a report template sample and a corresponding description document which meet the best practice specification;
the report template version control 42 is based on a Python Git library to realize the version control of the report template, and the versioning record of the report template can be realized based on a corresponding command every time the report template is updated;
the plugin and plugin library management 43 performs plugin and plugin library management based on the Conda software package management system, and is a set of online plugin warehouse, wherein the online plugin warehouse comprises various visual plugins developed by the community, and supports one-key installation of visual plugins of specified versions in the online plugin warehouse, so that plugin version management and reuse are realized.
The working principle of the interactive visual reporting system for displaying high throughput sequencing data analysis provided by the embodiment is as follows:
the report generation and connection module M1 and the plug-in module M2 convert the high-throughput sequencing data into an interactive visualization chart by using Python plug-in technology and Markdown grammar interpreter, and embed the interactive visualization chart into a static HMTL page, thereby generating an interactive visualization report. The report template editing module M3 provides the Markdown editor 31, the Web service unit 32 and the file monitoring unit 33 that support real-time editing by the user, so that the user can modify the report content online and render in real time to generate an interactive report, and help the user to continuously adjust the optimized report in a what-you-see-is-what-you-get manner.
As the user writes the report content, the user is usually faced with the requirements of visual plug-in installation and repeated generation of the report content in the same scene. Therefore, the management module M4 helps the user to quickly install and manage the visual plug-in and save the written report content as a template, which is convenient for quick report reuse in the same scene and improves the generation efficiency of similar reports.
The embodiments described above are described to facilitate an understanding and use of the invention by those skilled in the art. It will be readily apparent to those skilled in the art that various modifications to these embodiments may be made, and the generic principles described herein may be applied to other embodiments without the use of the inventive faculty. Therefore, the present invention is not limited to the above embodiments, and those skilled in the art should make improvements and modifications within the scope of the present invention based on the disclosure of the present invention.
Claims (10)
1. An interactive visual reporting system for displaying high throughput sequencing data results, comprising:
the report generation and connection module is used for connecting the Markdown report template, the multiple groups of mathematical data and the plug-in units and converting the report template into an online HTML report;
the report template editing module is used for performing online writing and debugging on the report template;
the plug-in module is used for realizing the dynamic loading and compiling of the plug-ins and providing corresponding plug-ins for the report template editing module;
and the management module is used for managing the traceable operation of the report template writing process and the generation process.
2. The interactive visual reporting system for displaying high throughput sequencing data results of claim 1 wherein said report generation and connection module comprises:
the plug-in grammar unit is used for generating custom plug-in grammar;
the Markdown interpreter calls the corresponding plug-in by identifying the self-defined plug-in grammar, transmits related parameters and data, and embeds a JavaScript code generated after the plug-in runs into a Markdown template in the form of a script tag; and according to a self-defined analysis rule, converting the related parameters and the data and finishing the rendering of Markdown and the generation of a report.
3. The interactive visual reporting system for displaying high throughput sequencing data results of claim 2 wherein said customized parsing rules comprise lexical parsing rules, syntactic parsing rules and code generation/execution rules.
4. The interactive visual reporting system for displaying high throughput sequencing data results of claim 3 wherein said parsing execution of said customized parsing rule comprises the steps of:
1) lexical analysis: recognizing the character string as a word sequence according to a word forming rule;
2) and (3) syntax analysis: combining the word sequences into phrases;
3) code generation/execution: and searching a corresponding plug-in according to the phrase, transmitting the parameter list obtained by analysis, initializing a plug-in class, processing the parameter list, caching all data files to a specified working directory, replacing a file path, calling a run method in a plug-in example to generate a JavaScript code related to a visual chart, and inserting the JavaScript code into a Markdown file specified position by a script tag.
5. The interactive visual reporting system for displaying high throughput sequenced data result of claim 2 wherein said custom plug-in grammar is a idiomatic grammar following function calls in a common language, said custom plug-in grammar comprising a plug-in and a parameter list, said plug-in being provided with a special character, said special character and plug-in name forming an identifier.
6. The interactive visual reporting system for displaying high throughput sequencing data results of claim 1 wherein said plug-in module comprises:
the plug-in dynamic loading unit is used for identifying the plug-ins meeting the requirements in the current environment and registering the plug-ins into a plug-in list for calling when a report is generated subsequently;
the interactive plug-in library stores various plug-ins of the plug-ins.
7. The interactive visual reporting system of claim 6 wherein the interactive plug-in repository stores a list plug-in, a perspective and perspective list plug-in, and an interactive visual graph plug-in.
8. The interactive visual reporting system of claim 7 wherein the interactive visual chart plug-in dynamically generates a dynamic chart for displaying reporting results using custom parametric control panels and real-time calculations.
9. The interactive visual reporting system for displaying high throughput sequencing data results of claim 1 wherein said report template editing module comprises:
the Web service unit is used for providing functions of downloading user registration channel data, modifying and rendering report files in real time and interactively displaying the report files;
the Markdown editor executes online editing, debugging and previewing of the Markdown text through the Web service unit;
and the file monitoring unit is used for judging whether the file is modified or not by monitoring the change of the report file in the specified directory.
10. The interactive visual reporting system for displaying high throughput sequencing data results of claim 1 wherein said management module comprises:
the report template sample generation tool provides a corresponding report template generation command for a user to generate a report template sample which accords with the best practice specification and a corresponding description document;
the report template version control is realized, and the version control of the report template is realized;
and the plug-in and plug-in library management unit is used for managing the interactive plug-in library and the plug-ins, and the plug-ins also comprise various visual plug-ins developed by the community and visual plug-ins of specified versions installed in the online plug-in warehouse by one key.
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Cited By (1)
| Publication number | Priority date | Publication date | Assignee | Title |
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| CN114627968A (en) * | 2022-03-18 | 2022-06-14 | 四川大学华西医院 | Multi-modal omics data management system |
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Cited By (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN114627968A (en) * | 2022-03-18 | 2022-06-14 | 四川大学华西医院 | Multi-modal omics data management system |
| CN114627968B (en) * | 2022-03-18 | 2023-10-20 | 四川大学华西医院 | Multi-mode histology data management system |
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