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README.md View File

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# 用户指南

## 克隆`choppy-docs`库

```
git clone http://choppy.3steps.cn/go-choppy/choppy-docs.git
```

<br>

## 目录介绍
- 文档源文件:包含可编写的 Markdown 文件的文件夹 `choppy-docs/docs`
- 博客:包含了可编写的 Markdown 文章的文件夹 `choppy-docs/website/blog`
- 页面:包含示例网站顶级页面的文件夹 `choppy-docs/website/pages`
- 静态资源与图片:包含供网站使用的静态资源文件夹 `choppy-docs/website/static`

<br>

## 关键文件
切莫删除或修改 choppy-docs/website/siteConfig.js 和 choppy-docs/website/core/Footer.js 文件
- 文档目录:`choppy-docs/website/sidebars.json` 文件包含文档文件的结构与排序,**十分关键**,所有文档源文件都需要记录到此文件才能够正常渲染出文档目录
- 页脚:`choppy-docs/website/core/Footer.js` 文件是一个 React 组件,用于生成 `choppy-docs` 站点的页脚,它可以由用户定制
- 配置文件:`choppy-docs/website/siteConfig.js` 文件是 `choppy-docs` 的主配置文件

<br>

## 修改文档/Blog
### Docs撰写
所有文档位于`choppy-docs/docs`目录,撰写规范如下:
- 将您的文档以 .md 文件的形式添加到 /docs 文件夹中,并确保每个文件都有正确的header。 最简单的标题如下,其中 id 是链接名称(例如 docs/intro.html),title 当然是浏览器页面的标题
```
---
id: intro
title: 入门
---
```

<br>

- 将零个或多个文档添加到 sidebars.json 文件,以便您的文档在侧边栏中呈现,如果您想要显示它们
> 如果您不将文档添加到 sidebars.json 文件中,那么文档依然被渲染,但只能从其他文档链接到该文档,并使用已知的URL进行访问
>
> 注意:sidebars.json文件中填写的均是id,而非 Markdown 文件名。sidebars.json文件依靠id来索引 Markdown 文件。

<br>

- 示例:
```json
{
"docs": {
"Choppy 简介": ["choppy-intro"],
"快速指南": ["quick-intro"],
"Cromwell": [],
"WDL 定义": ["wdl/wdl-intro"],
"Choppy App定义": [
"choppy_app/choppy-app-intro",
"choppy_app/choppy-app-vars",
"choppy_app/choppy-app-expression",
"choppy_app/choppy-app-filter",
"choppy_app/choppy-app-whitespace",
"choppy_app/choppy-app-condition",
"choppy_app/choppy-app-annotation"
]
}
```

<br>
- 将您的文档以 .md 文件的形式添加到 /docs 文件夹中,并确保每个文件都有正确的header。 最简单的标题如下,其中 id 是链接名称(例如 docs/intro.html),title 当然是浏览器页面的标题
```
---
id: intro
title: 入门
---
```

- 将零个或多个文档添加到 sidebars.json 文件,以便您的文档在侧边栏中呈现,如果您想要显示它们
> 如果您不将文档添加到 sidebars.json 文件中,那么文档依然被渲染,但只能从其他文档链接到该文档,并使用已知的URL进行访问
>
> 注意:sidebars.json文件中填写的均是id,而非 Markdown 文件名。sidebars.json文件依靠id来索引 Markdown 文件。

- 示例:
```json
{
"docs": {
"Choppy 简介": ["choppy-intro"],
"快速指南": ["quick-intro"],
"Cromwell": [],
"WDL 定义": ["wdl/wdl-intro"],
"Choppy App定义": [
"choppy_app/choppy-app-intro",
"choppy_app/choppy-app-vars",
"choppy_app/choppy-app-expression",
"choppy_app/choppy-app-filter",
"choppy_app/choppy-app-whitespace",
"choppy_app/choppy-app-condition",
"choppy_app/choppy-app-annotation"
]
}
```

### Blog撰写
位于`choppy-docs/website/blog`目录

- 添加博文
要在博客中发布,请在博客文件夹中创建一个格式为 YYYY-MM-DD-My-Blog-Post-Title.md 的文件。 发布日期是从文件名中提取的。
例如,在 website/blog/2017-08-18-Introducing-Docusaurus.md:
要在博客中发布,请在博客文件夹中创建一个格式为 YYYY-MM-DD-My-Blog-Post-Title.md 的文件。 发布日期是从文件名中提取的。例如,在 website/blog/2017-08-18-Introducing-Docusaurus.md:

```
---
@@ -84,19 +69,17 @@ git clone http://choppy.3steps.cn/go-choppy/choppy-docs.git
---
```

<br>

- Header 参数
唯一必需的字段是title; 不过,我们也提供了将作者信息添加到博客文章的参数。
- author - 作者署名的文本标签。
- authorURL - 与作者相关的网址。 这可能是一个Twitter,GitHub,Facebook帐户等。
- authorFBID - 用于提取个人资料图片的 Facebook ID。
- title - 博客文章标题。

<br>
唯一必需的字段是title; 不过,我们也提供了将作者信息添加到博客文章的参数。
- author - 作者署名的文本标签。
- authorURL - 与作者相关的网址。 这可能是一个Twitter,GitHub,Facebook帐户等。
- authorFBID - 用于提取个人资料图片的 Facebook ID。
- title - 博客文章标题。

- 摘要截断
使用博客文章中的 <!--truncate--> 标记来表示在查看博客发布的所有博客文章时将显示的摘要。 在 <!--truncate--> 之上的任何内容都将成为摘要的一部分。 例如:

使用博客文章中的 <!--truncate--> 标记来表示在查看博客发布的所有博客文章时将显示的摘要。 在 <!--truncate--> 之上的任何内容都将成为摘要的一部分。 例如:

```
---
@@ -114,4 +97,27 @@ git clone http://choppy.3steps.cn/go-choppy/choppy-docs.git
不是这里。
也不是这里。
```
```

## 启动文档 Server
```
# 切换工作目录
cd ./website

# 安装依赖环境
yarn install

# 启动 dev-server
yarn start

# build 静态网站
yarn build

# 构建并上传至阿里云OSS
yarn build && yarn upload
```

## FAQ
1. Cannot GET /
通常由于 Docusaurus 无法正确解析sidebars.json 文件所致。比如 id 引用不正确或者不是一个合格的markdown文件

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- [1.6 模板控制结构](choppy_app/5.控制结构.md)
- [1.7 模板注释](choppy_app/6.注释.md)
- [1.8 APP README撰写规范](choppy_app/7.APP_README模板.md)
- [第五章 阿里云批量计算](alicloud_batch_compute/)
- [第五章 Git指南](git/)
- [1.1 Git简介](git/[Git]01-Git简介.md)
- [1.2 Git的诞生](git/[Git]02-Git的诞生.md)
- [1.3 安装Git](git/[Git]03-安装Git.md)
- [1.4 创建版本库](git/[Git]04-创建版本库.md)
- [1.5 时光机穿梭](git/[Git]05-时光机穿梭.md)
- [1.6 版本回退](git/[Git]06-版本回退.md)
- [1.7 工作区与暂存区](git/[Git]07-工作区与暂存区.md)
- [1.8 管理修改](git/[Git]08-管理修改.md)
- [1.9 撤销修改](git/[Git]09-撤销修改.md)
- [1.10 删除文件](git/[Git]10-删除文件.md)
- [1.11 远程仓库](git/[Git]11-远程仓库.md)
- [1.12 添加远程仓库](git/[Git]12-添加远程仓库.md)
- [1.13 从远程仓库克隆](git/[Git]13-从远程仓库克隆.md)
- [1.14 分支管理](git/[Git]14-分支管理.md)
- [1.15 创建与合并分支](git/[Git]15-创建与合并分支.md)
- [1.16 解决冲突](git/[Git]16-解决冲突.md)
- [1.17 分支管理策略](git/[Git]17-分支管理策略.md)
- [1.18 Bug分支](git/[Git]18-Bug分支.md)
- [1.19 Feature分支](git/[Git]19-Feature分支.md)
- [1.20 多人协作](git/[Git]20-多人协作.md)
- [1.21 标签管理](git/[Git]21-标签管理.md)
- [1.22 创建标签](git/[Git]22-创建标签.md)
- [1.23 操作标签](git/[Git]23-操作标签.md)
- [第六章 Docker指南](docker/)
- [1.1 Docker简介](docker/docker简介.md)
- [1.2 Docker镜像构建](docker/docker镜像构建.md)
- [第七章 阿里云批量计算](alicloud_batch_compute/)
- [1.1 概述](alicloud_batch_compute/0.概述.md)
- [1.2 批量计算框架](alicloud_batch_compute/1.批量计算架构.md)
- [1.3 功能特性](alicloud_batch_compute/2.功能特性.md)
- [1.4 名词解释](alicloud_batch_compute/3.名词解释.md)
- [1.5 准备工作](alicloud_batch_compute/4.准备工作.md)
- [1.6 支持地域](alicloud_batch_compute/5.支持地域.md)
- [第六章 阿里云 OSS 存储](alicloud_oss/)
- [第章 阿里云 OSS 存储](alicloud_oss/)
- [1.1 什么是对象存储](alicloud_oss/0.什么是对象存储.md)
- [1.2 存储类型介绍](alicloud_oss/1.存储类型介绍.md)
- [1.3 访问域名和数据中心](alicloud_oss/2.访问域名和数据中心.md)

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@@ -12,14 +12,41 @@
- [1.6 模板控制结构](choppy_app/5.控制结构.md)
- [1.7 模板注释](choppy_app/6.注释.md)
- [1.8 APP README撰写规范](choppy_app/7.APP_README模板.md)
- [第五章 阿里云批量计算](alicloud_batch_compute/)
- [第五章 Git指南](git/)
- [1.1 Git简介](git/[Git]01-Git简介.md)
- [1.2 Git的诞生](git/[Git]02-Git的诞生.md)
- [1.3 安装Git](git/[Git]03-安装Git.md)
- [1.4 创建版本库](git/[Git]04-创建版本库.md)
- [1.5 时光机穿梭](git/[Git]05-时光机穿梭.md)
- [1.6 版本回退](git/[Git]06-版本回退.md)
- [1.7 工作区与暂存区](git/[Git]07-工作区与暂存区.md)
- [1.8 管理修改](git/[Git]08-管理修改.md)
- [1.9 撤销修改](git/[Git]09-撤销修改.md)
- [1.10 删除文件](git/[Git]10-删除文件.md)
- [1.11 远程仓库](git/[Git]11-远程仓库.md)
- [1.12 添加远程仓库](git/[Git]12-添加远程仓库.md)
- [1.13 从远程仓库克隆](git/[Git]13-从远程仓库克隆.md)
- [1.14 分支管理](git/[Git]14-分支管理.md)
- [1.15 创建与合并分支](git/[Git]15-创建与合并分支.md)
- [1.16 解决冲突](git/[Git]16-解决冲突.md)
- [1.17 分支管理策略](git/[Git]17-分支管理策略.md)
- [1.18 Bug分支](git/[Git]18-Bug分支.md)
- [1.19 Feature分支](git/[Git]19-Feature分支.md)
- [1.20 多人协作](git/[Git]20-多人协作.md)
- [1.21 标签管理](git/[Git]21-标签管理.md)
- [1.22 创建标签](git/[Git]22-创建标签.md)
- [1.23 操作标签](git/[Git]23-操作标签.md)
- [第六章 Docker指南](docker/)
- [1.1 Docker简介](docker/docker简介.md)
- [1.2 Docker镜像构建](docker/docker镜像构建.md)
- [第七章 阿里云批量计算](alicloud_batch_compute/)
- [1.1 概述](alicloud_batch_compute/0.概述.md)
- [1.2 批量计算框架](alicloud_batch_compute/1.批量计算架构.md)
- [1.3 功能特性](alicloud_batch_compute/2.功能特性.md)
- [1.4 名词解释](alicloud_batch_compute/3.名词解释.md)
- [1.5 准备工作](alicloud_batch_compute/4.准备工作.md)
- [1.6 支持地域](alicloud_batch_compute/5.支持地域.md)
- [第六章 阿里云 OSS 存储](alicloud_oss/)
- [第章 阿里云 OSS 存储](alicloud_oss/)
- [1.1 什么是对象存储](alicloud_oss/0.什么是对象存储.md)
- [1.2 存储类型介绍](alicloud_oss/1.存储类型介绍.md)
- [1.3 访问域名和数据中心](alicloud_oss/2.访问域名和数据中心.md)
@@ -28,3 +55,14 @@
- [1.6 基本概念介绍](alicloud_oss/5.基本概念介绍.md)
- [1.7 存储类型转换](alicloud_oss/6.存储类型转换.md)
- [1.8 创建和使用归档存储类型](alicloud_oss/7.创建和使用归档存储类型.md)
- [第九章 报告系统插件](plugins/)
- [1.1 boxplot-r](plugins/boxplot-r.md)
- [1.2 corrplot-r](plugins/corrplot-r.md)
- [1.3 data-table-js](plugins/data-table-js.md)
- [1.4 density-plot](plugins/density-plot.md)
- [1.5 group-boxplot](plugins/group-boxplot.md)
- [1.6 pivot-table-js](plugins/pivot-table-js.md)
- [1.7 rocket-plot-r](plugins/rocket-plot-r.md)
- [1.8 stack-barplot-r](plugins/stack-barplot-r.md)
- [1.9 upset-r](plugins/upset-r.md)
- [1.10 violin-plot-r](plugins/violin-plot-r.md)

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---
id: boxplot-r
title: boxplot-r
sidebar_label: boxplot-r
---

## `boxplot-r[choppy-report-plugin]`
### Description
Interactive boxplot visualization from a Shiny app(r version).

### Example Data
```
ScreenID Patient Protocol Site Birth Age Gender DoubleBlind_0to24 Extended_24to52 HbA1c_DF24to0
10010001 1001 CGZ301 1001 1972/12/7 41 Female Placebo Placebo_48mg 1.1
10010002 1002 CGZ301 1001 1951/10/8 62 Male CG_32mg CG_32mg 0.0
10010004 1003 CGZ301 1001 1956/1/27 58 Male Placebo Placebo_32mg 1.6
10010003 1004 CGZ301 1001 1956/2/13 58 Male CG_32mg CG_32mg -0.4
10010005 1005 CGZ301 1001 1952/2/23 62 Male CG_48mg CG_48mg -1.3
10010006 1006 CGZ301 1001 1973/10/6 40 Male CG_48mg CG_48mg -1.8
10030004 1007 CGZ301 1003 1979/2/5 35 Male CG_32mg CG_32mg -1.1
10030003 1010 CGZ301 1003 1982/5/23 32 Male Placebo Placebo_48mg -1.7
10030002 1011 CGZ301 1003 1970/4/4 44 Male Placebo Placebo_32mg -0.6
10030012 1012 CGZ301 1003 1957/8/20 57 Female CG_32mg CG_32mg -1.9
10110004 1013 CGZ301 1011 1974/2/28 40 Male CG_32mg CG_32mg -1.2
10110003 1014 CGZ301 1011 1961/7/26 53 Female Placebo Placebo_32mg -1.4
```

### Usage

```
@boxplot-r(dataFile='boxplot-r.rds', dataType='rds', title='',
xAxis='DoubleBlind_0to24', xTitle='DoubleBlind_0to24',
xAngle=90, yAxis='HbA1c_DF24to0', yTitle='HbA1c_DF24to0',
colorAttr='DoubleBlind_0to24', subtitle='', text='')
```

### Arguments

```ini
; input data, may be a file or other data source.
; input data must be tidy data.
dataFile = boxplot-r.rds
; data file format
dataType = rds
; Shiny app title
title =
; The column name from data frame for x axis attribute
xAxis = DoubleBlind_0to24
xTitle =
xAngle = 90
; The column name from data frame for y axis attribute
yAxis = HbA1c_DF24to0
yTitle =
; The column name from data frame for color attribute
colorAttr = DoubleBlind_0to24
; query url(unsupported in the current version.)
queryURL = https://www.duckduckgo.com/?q=
; subtitle and text for scatter chart
subtitle =
text =
```

### Value
An interactive boxplot.

### Author(s)
Jingcheng Yang(yjcyxky@163.com)

### Examples

```
# If you need to show a default interactive plot by using sample data
@boxplot-r()

# If you have a custom data, you need to reset these arguments at least.
@boxplot-r(dataFile='boxplot-r.rds', dataType='rds', xAxis='DoubleBlind_0to24',
yAxis='HbA1c_DF24to0')
```

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---
id: corrplot-r
title: corrplot-r
sidebar_label: corrplot-r
---

## `corrplot-r[choppy-report-plugin]`
### Description
Interactive correlation plot visualization from a Shiny app(r version).

### Example Data
```
Stage ReadCount Sample.ID StageGroup
Adapter Only 2178202 A-QI-1-1 1
Adapter Only 706077 A-QI-1-2 1
Adapter Only 1674179 A-QI-1-3 1
Adapter Only 991912 B-QI-1-1 1
Adapter Only 889332 B-QI-1-2 1
Adapter Only 677786 B-QI-1-3 1
Adapter Only 286820 P10-QI-4-1 1
Adapter Only 805699 P10-QI-4-2 1
Adapter Only 766579 P10-QI-4-3 1
Adapter Only 104417 P10-QI-4-4 1
Adapter Only 113903 P10-QI-4-5 1
```

### Usage

```
@stack-barplot-r(dataFile='stack-barplot-example.rds', dataType='rds', title='',
xAxis='Sample.ID', xTitle='Sample.ID', yAxis='ReadCount', yTitle='ReadCount',
xAngle=90, labelAttr='Stage', subtitle='', text='', barPos='fill',
smartColor='StageGroup')
```

### Arguments

```ini
; Configuration for stack barplot
[data]
; input data, may be a file or other data source.
; input data must be tidy data.
dataFile = stack-barplot-example.rds
; data file format
dataType = rds

[attributes]
; Shiny app title
title =
; The column name from data frame for x axis attribute
xAxis = Sample.ID
xTitle =
xAngle = 90
; The column name from data frame for y axis attribute
yAxis = ReadCount
yTitle =
labelAttr = Stage
; query url
queryURL = https://www.duckduckgo.com/?q=
; subtitle and text for scatter chart
subtitle =
text =
; Bar position, choices: fill, dodge, stack
barPos = fill
; The column name from data frame for smart color attribute
smartColor = StageGroup
```

### Value
An interactive stack barplot.

### Author(s)
Jingcheng Yang(yjcyxky@163.com)

### Examples

```
# If you need to show a default interactive plot by using sample data
@stack-barplot-r()

# If you have a custom data, you need to reset these arguments at least.
@stack-barplot-r(dataFile='stack-barplot-example.rds', dataType='rds',
xAxis='Sample.ID', yAxis='ReadCount')
```

+ 50
- 0
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@@ -0,0 +1,50 @@
---
id: data-table-js
title: data-table-js
sidebar_label: data-table-js
---

## `data-table-js[choppy-report-plugin]`
### Description
Another interactive data table. It is based on datatables js library.

### Example Data
```
Stage ReadCount Sample.ID StageGroup
Adapter Only 2178202 A-QI-1-1 1
Adapter Only 706077 A-QI-1-2 1
Adapter Only 1674179 A-QI-1-3 1
Adapter Only 991912 B-QI-1-1 1
Adapter Only 889332 B-QI-1-2 1
Adapter Only 677786 B-QI-1-3 1
Adapter Only 286820 P10-QI-4-1 1
Adapter Only 805699 P10-QI-4-2 1
Adapter Only 766579 P10-QI-4-3 1
Adapter Only 104417 P10-QI-4-4 1
Adapter Only 113903 P10-QI-4-5 1
```

### Usage

```
@data-table-js(dataUrl='stack-barplot-example.csv')
```

### Arguments

```text
dataUrl: [string] Your own file with CSV data by specifying the URL/Local Path to your file.
```

### Value
An interactive data table.

### Author(s)
Jingcheng Yang(yjcyxky@163.com)

### Examples

```
# If you have a custom data, you need to reset these arguments at least.
@data-table-js(dataUrl='stack-barplot-example.csv')
```

+ 75
- 0
docs/plugins/density-plot.md View File

@@ -0,0 +1,75 @@
---
id: density-plot
title: density-plot
sidebar_label: density-plot
---

## `density-plot[choppy-report-plugin]`
### Description
Interactive density plot visualization from a Shiny app(r version).

### Example Data
```
ScreenID Patient Protocol Site Birth Age Gender DoubleBlind_0to24 Extended_24to52 HbA1c_DF24to0
10010001 1001 CGZ301 1001 1972/12/7 41 Female Placebo Placebo_48mg 1.1
10010002 1002 CGZ301 1001 1951/10/8 62 Male CG_32mg CG_32mg 0.0
10010004 1003 CGZ301 1001 1956/1/27 58 Male Placebo Placebo_32mg 1.6
10010003 1004 CGZ301 1001 1956/2/13 58 Male CG_32mg CG_32mg -0.4
10010005 1005 CGZ301 1001 1952/2/23 62 Male CG_48mg CG_48mg -1.3
10010006 1006 CGZ301 1001 1973/10/6 40 Male CG_48mg CG_48mg -1.8
10030004 1007 CGZ301 1003 1979/2/5 35 Male CG_32mg CG_32mg -1.1
10030003 1010 CGZ301 1003 1982/5/23 32 Male Placebo Placebo_48mg -1.7
10030002 1011 CGZ301 1003 1970/4/4 44 Male Placebo Placebo_32mg -0.6
10030012 1012 CGZ301 1003 1957/8/20 57 Female CG_32mg CG_32mg -1.9
10110004 1013 CGZ301 1011 1974/2/28 40 Male CG_32mg CG_32mg -1.2
10110003 1014 CGZ301 1011 1961/7/26 53 Female Placebo Placebo_32mg -1.4
```

### Usage

```
@density-plot(dataFile='dt_toplot.rds', dataType='rds', title='',
xAxis='DoubleBlind_0to24', xTitle='DoubleBlind_0to24',
colorAttr='DoubleBlind_0to24', subtitle='', text='',
fillEnable=True)
```

### Arguments

```ini
; input data, may be a file or other data source.
; input data must be tidy data.
dataFile = boxplot-r.rds
; data file format
dataType = rds
; Shiny app title
title =
; The column name from data frame for x axis attribute
xAxis = DoubleBlind_0to24
xTitle =
; The column name from data frame for color attribute
colorAttr = DoubleBlind_0to24
; query url(unsupported in the current version.)
queryURL = https://www.duckduckgo.com/?q=
; Fill color or not
fillEnable = True
; subtitle and text for scatter chart
subtitle =
text =
```

### Value
An interactive density plot.

### Author(s)
Jingcheng Yang(yjcyxky@163.com)

### Examples

```
# If you need to show a default interactive plot by using sample data
@density-plot()

# If you have a custom data, you need to reset these arguments at least.
@density-plot(dataFile='boxplot-r.rds', dataType='rds', xAxis='DoubleBlind_0to24')
```

+ 90
- 0
docs/plugins/group-boxplot.md View File

@@ -0,0 +1,90 @@
---
id: group-boxplot
title: group-boxplot
sidebar_label: group-boxplot
---

## `group-boxplot[choppy-report-plugin]`
### Description
Interactive group-boxplot visualization from a Shiny app(r version).

### Example Data
```
group variable value
level1 LCL5 0.0001517905
level1 LCL5 0.0001362790
level1 LCL5 0.0001263074
level1 LCL5 0.0001495745
level1 LCL5 0.0001296313
level1 LCL5 0.0002614785
level1 LCL5 0.0001983248
level1 LCL5 0.0001407109
level1 LCL5 0.0001329551
level5 patients 0.1844907818
level5 patients 0.1848652721
level5 patients 0.1793886279
level5 patients 0.1789997341
level5 patients 0.1771848963
level5 patients 0.1828177628
level5 patients 0.1822936979
level5 patients 0.1806162471
level5 patients 0.1804711044
level5 patients 0.1751396029
```

### Usage

```
@group-boxplot(dataFile='dt_toplot.rds', dataType='rds', title='',
xAxis='group', xTitle='Group', yAxis='value', yTitle='Discordance',
colorAttr='variable', labelAttr='labels', legendTitle='Samples',
subtitle='', text='')
```

### Arguments

```ini
; Configuration for group boxplot
[data]
; input data, may be a file or other data source.
; input data must be tidy data.
dataFile = dt_toplot.rds
; data file format
dataType = rds

[attributes]
; Shiny app title
title =
; The column name from data frame for x axis attribute
xAxis = group
xTitle =
; The column name from data frame for y axis attribute
yAxis = value
yTitle =
; The column name from data frame for color attribute
colorAttr = variable
; The column name from data frame for point label
labelAttr = labels
legendTitle = Samples
; query url
queryURL = https://www.duckduckgo.com/?q=
; subtitle and text for scatter chart
subtitle =
text =
```

### Value
An interactive group box plot.

### Author(s)
Jingcheng Yang(yjcyxky@163.com)

### Examples

```
# If you need to show a default interactive plot by using sample data
@group-boxplot()

# If you have a custom data, you need to reset these arguments at least.
@group-boxplot(dataFile='dt_toplot.rds', dataType='rds', xAxis='group', yAxis='value')
```

+ 54
- 0
docs/plugins/pivot-table-js.md View File

@@ -0,0 +1,54 @@
---
id: pivot-table-js
title: pivot-table-js
sidebar_label: pivot-table-js
---

## `pivot-table-js[choppy-report-plugin]`
### Description
Interactive pivot-table and pivot-chart. It is based on webdatarocks and highcharts.

### Example Data
```
Stage ReadCount Sample.ID StageGroup
Adapter Only 2178202 A-QI-1-1 1
Adapter Only 706077 A-QI-1-2 1
Adapter Only 1674179 A-QI-1-3 1
Adapter Only 991912 B-QI-1-1 1
Adapter Only 889332 B-QI-1-2 1
Adapter Only 677786 B-QI-1-3 1
Adapter Only 286820 P10-QI-4-1 1
Adapter Only 805699 P10-QI-4-2 1
Adapter Only 766579 P10-QI-4-3 1
Adapter Only 104417 P10-QI-4-4 1
Adapter Only 113903 P10-QI-4-5 1
```

### Usage

```
@pivot-table-js(dataUrl='stack-barplot-example.csv', enableLocal=False)
```

### Arguments

```text
dataUrl: [string] Your own file with JSON or CSV data by specifying the URL/Local Path to your file.
enableLocal: [boolean] If enable to upload local file from users' computer. default is False
```

### Value
An interactive pivot-table and pivot-chart.

### Author(s)
Jingcheng Yang(yjcyxky@163.com)

### Examples

```
# If you have a custom data, you need to reset these arguments at least.
@pivot-table-js(dataUrl='stack-barplot-example.csv')

# If you want to enable user to upload file, you need to use enableLocal argument.
@pivot-table-js(dataUrl='stack-barplot-example.csv', enableLocal=True)
```

+ 80
- 0
docs/plugins/rocket-plot-r.md View File

@@ -0,0 +1,80 @@
---
id: rocket-plot-r
title: rocket-plot-r
sidebar_label: rocket-plot-r
---

## `rocket-plot-r[choppy-report-plugin]`
### Description
Interactive rocket plot visualization from a Shiny app(r version).

### Example Data
```
ID.miRNA A.QI.1.1 A.QI.1.2 A.QI.1.3 B.QI.1.1 B.QI.1.2 B.QI.1.3
hsa-let-7a-5p 17.229546 17.5298890 17.450287 17.6053028 17.418615 17.4270934
hsa-let-7b-5p 17.003783 17.2648570 17.177195 17.3531438 17.135108 17.2305650
hsa-let-7c-5p 14.730315 15.8122775 14.963884 15.9381663 14.891995 15.8957725
hsa-let-7d-5p 12.729670 12.7560022 12.903733 12.7636084 12.860683 12.7553675
hsa-let-7e-5p 14.358456 14.2749982 14.480325 14.3446585 14.573276 14.1889370
hsa-let-7f-5p 14.130429 15.8313783 14.005740 15.7909300 14.097287 15.6946755
hsa-let-7g-5p 13.224542 13.8243976 13.427797 13.8694199 13.304371 13.9239037
hsa-let-7i-5p 16.675953 15.0214654 16.619071 15.0821202 16.534948 15.1626320
```

### Usage

```
@rocket-plot-r(dataFile='rocket_plot.rds', dataType='rds', title='',
xAxis='A.QI.1.1', xTitle='A.QI.1.1', yAxis='A.QI.1.3', yTitle='A.QI.1.3',
xAngle=0, labelAttr='ID.miRNA', method='None', pointAlpha=1,
pointSize=1, subtitle='', text='')
```

### Arguments

```ini
; Configuration for rocket plot
[data]
; input data, may be a file or other data source.
; input data must be tidy data.
dataFile = rocket_plot.rds
; data file format
dataType = rds

[attributes]
; Shiny app title
title =
; The column name from data frame for x axis attribute
xAxis = A.QI.1.1
xTitle =
xAngle = 0
; The column name from data frame for y axis attribute
yAxis = A.QI.1.3
yTitle =
labelAttr = ID.miRNA
; query url
queryURL = https://www.duckduckgo.com/?q=
; support None, linear_regression, pearson_correlation
method = None
; subtitle and text for scatter chart
subtitle =
text =
pointAlpha = 1
pointSize = 1.5
```

### Value
An interactive rocket plot.

### Author(s)
Jingcheng Yang(yjcyxky@163.com)

### Examples

```
# If you need to show a default interactive plot by using sample data
@rocket-plot-r()

# If you have a custom data, you need to reset these arguments at least.
@rocket-plot-r(dataFile='rocket_plot.rds', dataType='rds', xAxis='A.QI.1.1', yAxis='A.QI.1.3')
```

+ 84
- 0
docs/plugins/stack-barplot-r.md View File

@@ -0,0 +1,84 @@
---
id: stack-barplot-r
title: stack-barplot-r
sidebar_label: stack-barplot-r
---

## `stack-barplot-r[choppy-report-plugin]`
### Description
Interactive stack barplot visualization from a Shiny app(r version).

### Example Data
```
Stage ReadCount Sample.ID StageGroup
Adapter Only 2178202 A-QI-1-1 1
Adapter Only 706077 A-QI-1-2 1
Adapter Only 1674179 A-QI-1-3 1
Adapter Only 991912 B-QI-1-1 1
Adapter Only 889332 B-QI-1-2 1
Adapter Only 677786 B-QI-1-3 1
Adapter Only 286820 P10-QI-4-1 1
Adapter Only 805699 P10-QI-4-2 1
Adapter Only 766579 P10-QI-4-3 1
Adapter Only 104417 P10-QI-4-4 1
Adapter Only 113903 P10-QI-4-5 1
```

### Usage

```
@stack-barplot-r(dataFile='stack-barplot-example.rds', dataType='rds', title='',
xAxis='Sample.ID', xTitle='Sample.ID', yAxis='ReadCount', yTitle='ReadCount',
xAngle=90, labelAttr='Stage', subtitle='', text='', barPos='fill',
smartColor='StageGroup')
```

### Arguments

```ini
; Configuration for stack barplot
[data]
; input data, may be a file or other data source.
; input data must be tidy data.
dataFile = stack-barplot-example.rds
; data file format
dataType = rds

[attributes]
; Shiny app title
title =
; The column name from data frame for x axis attribute
xAxis = Sample.ID
xTitle =
xAngle = 90
; The column name from data frame for y axis attribute
yAxis = ReadCount
yTitle =
labelAttr = Stage
; query url
queryURL = https://www.duckduckgo.com/?q=
; subtitle and text for scatter chart
subtitle =
text =
; Bar position, choices: fill, dodge, stack
barPos = fill
; The column name from data frame for smart color attribute
smartColor = StageGroup
```

### Value
An interactive stack barplot.

### Author(s)
Jingcheng Yang(yjcyxky@163.com)

### Examples

```
# If you need to show a default interactive plot by using sample data
@stack-barplot-r()

# If you have a custom data, you need to reset these arguments at least.
@stack-barplot-r(dataFile='stack-barplot-example.rds', dataType='rds',
xAxis='Sample.ID', yAxis='ReadCount')
```

+ 77
- 0
docs/plugins/upset-r.md View File

@@ -0,0 +1,77 @@
---
id: upset-r
title: upset-r
sidebar_label: upset-r
---

## `upset-r[choppy-report-plugin]`
### Description
Interactive upset plot visualization from a Shiny app(r version).

### Example Data
```
Name ReleaseDate Action Adventure Children
Toy Story (1995) 1995 0 0 1
Jumanji (1995) 1995 0 1 1
Grumpier Old Men (1995) 1995 0 0 0
Waiting to Exhale (1995) 1995 0 0 0
Father of the Bride Part II (1995) 1995 0 0 0
Heat (1995) 1995 1 0 0
Sabrina (1995) 1995 0 0 0
Tom and Huck (1995) 1995 0 1 1
Sudden Death (1995) 1995 1 0 0
GoldenEye (1995) 1995 1 1 0
```

### Usage

```
@upset-r(dataFile='movies.rds', dataType='rds', title='',
showEmptyInterSec=True, showBarNumbers=True, setSort=True,
nIntersects=10, assignmentType='upset', subtitle='', text='',
showpanel=True)
```

### Arguments

```ini
; Configuration for Scatter Chart
[data]
; input data, may be a file or other data source.
; input data must be tidy data.
dataFile = movies.rds
; data file format
dataType = rds

[attributes]
; Shiny app title
title =
showEmptyInterSec = True
showBarNumbers = True
setSort = True
nIntersects = 10
; choices: ('upset', 'all')
assignmentType = upset
; query url
queryURL = https://www.duckduckgo.com/?q=
; subtitle and text for scatter chart
subtitle =
text =
showpanel = True
```

### Value
An interactive upset plot.

### Author(s)
Jingcheng Yang(yjcyxky@163.com)

### Examples

```
# If you need to show a default interactive plot by using sample data
@upset-r()

# If you have a custom data, you need to reset these arguments at least.
@upset-r(dataFile='violin_plot.rds', dataType='rds')
```

+ 81
- 0
docs/plugins/violin-plot-r.md View File

@@ -0,0 +1,81 @@
---
id: violin-plot-r
title: violin-plot-r
sidebar_label: violin-plot-r
---

## `violin-plot-r[choppy-report-plugin]`
### Description
Interactive violin plot visualization from a Shiny app(r version).

### Example Data
```
TP53 KRAS EGFR OS_Status OS_Time age stage
4.827859 3.217293 3.035919 0 2973 66 stage_I
3.611481 2.940355 3.114689 0 3674 57 stage_IV
4.012998 2.947884 3.449437 1 1147 64 stage_II
3.282482 2.723632 3.568452 1 1357 42 stage_IV
5.054779 2.640598 2.404610 0 1324 65 stage_IV
3.443296 3.516531 3.841558 0 1351 74 stage_II
3.839475 2.759294 3.391223 0 1159 69 stage_II
3.722616 3.335489 3.691214 0 1280 65 stage_IV
4.410951 3.085761 3.154411 0 1301 55 stage_II
2.429508 3.847008 4.858569 1 761 51 stage_II
4.585097 2.788753 3.284768 0 1130 74 stage_III
3.791531 3.455349 2.447410 0 1163 77 stage_IV
```

### Usage

```
@violin-plot-r(dataFile='violin_plot.rds', dataType='rds', title='',
xAxis='stage', xTitle='stage', yAxis='age', yTitle='age',
xAngle=45, colorAttr='stage', subtitle='', text='')
```

### Arguments

```ini
; Configuration for violin_plot.
[data]
; input data, may be a file or other data source.
; input data must be tidy data.
dataFile = violin_plot.rds
; data file format
dataType = rds

[attributes]
; Shiny app title
title =
; The column name from data frame for x axis attribute
xAxis = stage
xTitle = stage
xAngle = 45
; The column name from data frame for y axis attribute
yAxis = age
yTitle = age
; The column name from data frame for color attribute
colorAttr = stage
; query url
queryURL = https://www.duckduckgo.com/?q=
; subtitle and text for violin plot
subtitle =
text =
```

### Value
An interactive violin plot.

### Author(s)
Jingcheng Yang(yjcyxky@163.com)

### Examples

```
# If you need to show a default interactive plot by using sample data
@violin-plot-r()

# If you have a custom data, you need to reset these arguments at least.
@violin-plot-r(dataFile='violin_plot.rds', dataType='rds',
xAxis='stage', yAxis='age')
```

+ 1
- 6
website/package.json View File

@@ -1,13 +1,8 @@
{
"scripts": {
"examples": "docusaurus-examples",
"start": "docusaurus-start",
"build": "docusaurus-build",
"upload": "cd ./build/Choppy/ && ossutilmac64 cp -r -u ./ oss://choppy-docs/",
"publish-gh-pages": "docusaurus-publish",
"write-translations": "docusaurus-write-translations",
"version": "docusaurus-version",
"rename-version": "docusaurus-rename-version"
"upload": "cd ./build/Choppy/ && ossutilmac64 -c ~/.oss/.ossutilconfig cp -r -u ./ oss://choppy-docs/"
},
"devDependencies": {
"docusaurus": "^1.6.2"

website/pages/zh_CN/help.js → website/pages/en/help.js View File


website/pages/zh_CN/index.js → website/pages/en/index.js View File


website/pages/zh_CN/users.js → website/pages/en/users.js View File


+ 13
- 4
website/sidebars.json View File

@@ -39,10 +39,7 @@
"git/git-tag-creation",
"git/git-handle-tag"
],
"Docker 指南": [
"docker/docker-intro",
"docker/choppy-docker-intro"
],
"Docker 指南": ["docker/docker-intro", "docker/choppy-docker-intro"],
"阿里云批量计算": [
"alicloud_batch_compute/bc-intro",
"alicloud_batch_compute/bc-framework",
@@ -60,6 +57,18 @@
"alicloud_oss/oss-basic-concepts",
"alicloud_oss/oss-storage-type-transform",
"alicloud_oss/oss-archive-type"
],
"报告系统插件": [
"plugins/boxplot-r",
"plugins/corrplot-r",
"plugins/data-table-js",
"plugins/density-plot",
"plugins/group-boxplot",
"plugins/pivot-table-js",
"plugins/rocket-plot-r",
"plugins/stack-barplot-r",
"plugins/upset-r",
"plugins/violin-plot-r"
]
},
"docs-other": {}

+ 13
- 4
website/siteConfig.js View File

@@ -28,7 +28,6 @@ const users = [
}
];


const siteConfig = {
title: "Choppy for Reproducible Omics Pipeline", // Title for your website.
tagline: "可重复性分析管理器",
@@ -47,11 +46,16 @@ const siteConfig = {

// For no header links in the top nav bar -> headerLinks: [],
headerLinks: [
{ search: true },
{ doc: "choppy-intro", label: "Docs" },
// { doc: 'doc4', label: 'API' },
{ page: 'help', label: 'Help' },
{ page: "help", label: "Help" },
// { blog: true, label: "Blog" },
{ blog: true, href: "http://docs.3steps.cn/blog/index.html", label: "Blog" },
{
blog: true,
href: "http://docs.3steps.cn/blog/index.html",
label: "Blog"
},
// Links to choppy destination
{ href: "http://choppy.3steps.cn", label: "App Store" },
{ languages: true }
@@ -71,6 +75,11 @@ const siteConfig = {
secondaryColor: "#205C3B"
},

algolia: {
apiKey: "438cbe6b6eb562459b61577f2b795c47",
indexName: "choppy"
},

/* Custom fonts for website */
/*
fonts: {
@@ -119,7 +128,7 @@ const siteConfig = {
enableUpdateTime: true,

// Google Analytics tracking ID to track page views.
gaTrackingId: 'go-choppy',
gaTrackingId: "go-choppy",

// Set this to true if you want to use global site tags (gtag.js) for Google analytics instead of analytics.js.
gaGtag: true,

BIN
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