MHA Instruction for Use (English)
1. Main Contents of MHA
- HOME: Introduction of the MHA database, updates, and references.
- DATASETS: Functional page of the MHA, where users can select data sets to be displayed visually.
- ABOUT: Help and manual for using MHA.
- AUTHORS: Information on the authors of the MHA.
2. Dataset Selection
- l In the DATASETS page, user can select an interesting dataset and wait 5-20 seconds for data loading (depending on the size of the dataset).
- l When a dataset is loaded, a schema diagram (Experiment Design), its associated disease (or physiological processes) and cell naming abbreviations can be seen.
3. Dimensional Reduction Plot
- Dimensional Reduction Plot. a: show all palettes which can be selected. b: show the ratio of each cell cluster. c: tSNE or umap dimensional reduction can be selected, and the cells (dots) are labeled according to their “cell_type” information for mapping (left panel). d: select the palette for the left panel. e: select the cell grouping method of the right panel, such as cell type, sample source or disease type, etc. f: Select the palette for the right panel. g: click to download the output image result (higher resolution), it can also be saved by “right-click” and “save as” (lower resolution).
4. Single Gene Expression Information
In this section, we provide two output methods including cell dimension reduction plot and violin plot, and users can choose the grouping method and palette of cells by themselves.
- Single gene expression with dimensional reduction plot. a: Manually input or select the target gene. b: Select the cell grouping method of dimensional reduction plot, such as cell type, sample source or disease type, etc. All cells in this dataset will be displayed in one plot if select NULL. c: Select the color scale bar representing the level of gene expression. d: Click to download the different expression genes list between groups of this dataset.
Violin plot of one single gene expression. a: select the cell grouping method of the violin plot (X-axis), generally, only the default grouping method of “cell_type” is provided; b: select the group comparison method of violin plot (each column split by what), including sample source or disease type, etc. c: select the color scheme of different split groups within one cell type; d: click to download the PDF file results.
Note: When the percentage of positive cell of target genes was very low, the width of the violin plot column often reducing to a line, so it was more suitable to choose a dimensional reduction plot or dot plot to display.
5. Multiple Gene Expression Information
In order to display the information of multiple genes, we also provide the output method of dot plot.
- Dot plot. a: users can manually input or select multiple genes to be displayed. b: select the cell grouping method of dot plot. c: Select the group comparison method of dot plot, including sample source or disease types, etc. (the X axis group is named as “Group by _ Split by”). d: select the color scale bar of the gene expression level; e: click to generate dot plot. f: click to download the result PDF file.
6. FAQ
6.1 I could not find the page titles (HOME DATASETS ABOUT AUTHORS) in the home page.
Solution: The user can re-display the hidden page titles by Setting -ZOOM in the browser. In addition, some mobile phones directly open the website in WeChat may also cause the above problems, can be solved by opening in the browser.
6.2 I could not input gene name in drop-down menu of the “Single gene expression information” section.
Solution: The user should delete the “Choose” in the drop-down menu before inputting.
7. Others
For more help and information about MHA, please contact author via zlyinwangyi@163.com.
MHA 数据库使用说明(中文)
1. 网站说明
- MHA首页:用于展示MHA数据库的简单介绍、更新和相关的引用信息。
- 数据展示页:MHA的主要内容,用户可在本栏选择数据集进行可视化展示。
- 网站介绍页:帮助与介绍信息。
- 作者介绍页:MHA网站的主要建设参与者信息。
2. 数据选择
- 在数据展示页(DATASETS),选择相应的数据集,等待5~20秒数据加载(时间根据数据集大小变化)。
- 数据集加载后,可看见该数据集的模式图、相关疾病(或生理发育过程)与细胞命名缩写规则。
3. 单细胞聚类与降维散点图
- 细胞聚类与降维散点图。a: 展示所有可供选择的配色方案;b:计算并显示各细胞群所占比例;c:可选择tSNE或者umap两种降维方式,作图使用默认细胞分组;d:选择左侧散点图的配色; e:选择右侧散点图的细胞分组方式,包括细胞类型、样本来源或疾病分组等;f:选择右侧散点图的配色;g:点击可下载输出的图片结果(分辨率较高),该结果同样可使用右键-另存为方式保存(分辨率较低)。
4. 单基因展示
在此部分,每次可展示一个基因的表达特征信息。我们提供细胞降维散点图和小提琴图两种结果输出方式,用户可自行选择细胞的分组方式和配色方案等。
- 单基因表达散点图。a:手动输入或选择目标基因;b:选择散点图的细胞分组方式,包括细胞类型、样本来源或疾病分组等,NULL代表默认不进行分组展示所有细胞;c:选择代表基因表达高低的配色方案;d:点击下载本数据集各类细胞或者各组间差异基因。
单基因表达小提琴图。a:选择小提琴图的细胞分组方式(X轴),一般只提供细胞类型的默认分组;b:选择小提琴图的同组对比方式,包括样本来源或疾病分组等;c:选择同细胞类型不同对比组的配色方案;d:点击下载小提琴图结果PDF文件。
注:当组的目标基因阳性表达占比较低时,小提琴图宽度缩小为一条线,此时可选用细胞降维散点图或者气泡图展示更为合理。
5. 多基因展示
为了方便展示多个基因的信息,我们在此部分提供了气泡图的结果输出方式。
- 基因表达气泡图。a:用户可以手动输入或选择多个待展示基因。b:选择气泡图的细胞分组方式,一般只提供细胞类型的默认分组;c:选择气泡图的同组对比方式,包括样本来源或疾病分组等(X轴各组名称以“分组方式_对比方式”命名);d:选择代表基因表达高低的配色方案;e:点击生成气泡图;f:点击下载结果文件。
6. 常见问题
6.1 在首页中看不见各个分页标签 (HOME DATASETS ABOUT AUTHORS)
解决方法:用户可以调整浏览器设置-缩放显示分页标题。另外,部分手机在微信中直接打开本网站也可能出现上述问题,可以通过在浏览器中打开解决。
6.2 在单基因展示部分,无法在下拉菜单中输入基因名
解决方法:下拉菜单中默认基因名为“Choose”,用户需要先删除下拉菜单中内容后,才可以输入新内容。
7. 其他
其他问题或者建议,欢迎通过邮箱zlyinwangyi@163.com联系作者。