# 2.3.5 工具 | 2018-iSEE：单细胞数据可视化辅助网页工具 ## 前言 题目：iSEE: Interactive SummarizedExperiment Explorer 日期：2018-06-14 期刊：F1000Research 链接： GitHub： 这篇文章虽然发表的比较早，但最近看到其中一个作者Federico Marini和大佬们交流hdf5数据支持的问题，所以还是简单了解一下这个工具吧 ![image-20211027125344809](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2021-10-27-045345.png) 他们讨论的结果是 ``` library(zellkonverter) sce_h5ad <- readH5AD("file_as_anndata.h5ad") assayNames(sce_h5ad) <- "logcounts" HDF5Array::saveHDF5SummarizedExperiment(sce_Bcells_h5ad, dir = "see_as_hdf5") #And to read that in -> sce_read_in_again <- HDF5Array::loadHDF5SummarizedExperiment("see_as_hdf5") library(iSEE) iSEE(sce_read_in_again) ``` ## 设计初衷 > 重在数据展示，而非数据分析 它不是单纯为某一个课题设计的网页工具，而只要是`SummarizedExperiment`它就可以支持可视化，而我们知道单细胞数据不仅仅是seurat格式，还有很大部分是`SummarizedExperiment` 。当然，除了单细胞，`SummarizedExperiment` 在其他领域（比如甲基化）也有涉及，因此这个工具可以无缝衔接支持此格式的R包下游，用来展示rowdata、metadata等。可以说，它最大的亮点就是兼容性和可拓展性 那么它为何对`SummarizedExperiment`格式这么偏爱呢？ 就像我之前在公众号里介绍的，这个对象可以整合 基因组信息（行）以及样本信息（列），并且可以容纳多种表达量类型（比如raw count、normalized count），甚至后期分析的结果也可以存储（比如降维结果） ![image-20211027130031898](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2021-10-27-050032.png) ## 工具结构 ![image-20211027130553046](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2021-10-27-050553.png) * **Column data plots**, for visualising sample metadata stored in the colData slot of the SummarizedExperiment object. * **Feature assay plots**, for visualising experimental observations for a particular feature (e.g. gene) across samples from any assay in the SummarizedExperiment object. * **Row statistics tables**, to present the contents of the rowData slot of the SummarizedExperiment object. * **Row data plots**, for visualising feature metadata stored in the rowData slot of the SummarizedExperiment object. * **Heatmaps**, to visualise assay data for multiple features where samples are ordered by one or more colData fields. * **Reduced dimension plots**, which display any two dimensions from pre-computed dimensionality reduction results (e.g., from PCA or *t*-SNE). These results are taken from the reducedDim slot if this is available in the object supplied to iSEE. 还设置了大量的参数调节，比如可以对这个数据的列数据进行选取： ![image-20211027130653904](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2021-10-27-050654.png) 目前提供了一些数据作为示例： * * * * * 还支持TCGA数据的可视化 ![image-20211027133643944](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2021-10-27-053644.png) ## 至于怎么实现的可视化 作者提供了一些rmd作为参考： ![image-20211027134159378](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2021-10-27-054159.png) ``` # 上游分析得到sce对象 # Once the processing steps above are done, we can call `iSEE` with the subsampled `SingleCellExperiment` object. if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("iSEE") # or also... BiocManager::install("iSEE", dependencies = TRUE) if (require(iSEE)) { iSEE(sce) } ``` --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://jieandze1314.osca.top/02/2.3.5-gong-ju-2018isee-dan-xi-bao-shu-ju-ke-shi-hua-fu-zhu-wang-ye-gong-ju.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.