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YuLab-SMU / ProjectYulab

:next_track_button: Small coding tasks that enable you to participate in our development
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customize upset plot with aplot #3

Open GuangchuangYu opened 1 year ago

GuangchuangYu commented 1 year ago

We can consider the upset plot as a composite plot, where each part can be drawn in the way that suits your needs, and then pieced together using aplot.

For example, the intersection part does not necessarily have to be drawn as the size of the intersection, it can be a feature of the intersection, such as the distribution of gene expression in the intersection. Of couse, for using aplot to create composite plots, you can also draw both the intersection size and feature together.

GZZHY79 commented 1 year ago

老师好，我是刚刚开始学习生信，在公众号看到了您对这个项目的介绍，我想尝试一下，但是因为是新手，没有任何经验，关于这个问题您有推荐参考的书目或者论文吗，谢谢老师

GuangchuangYu commented 1 year ago

@GZZHY79 如果你是研究生的话，我想你应该清楚的。如果是本科生的话，那么提前体验。

如果比喻为学游泳，那就是直接扔水里，自己扑腾去吧。不要想着我学点什么，然后我就能干什么。趁早断了这念头。

要靠自己去探索，这个task，如果说有什么可以参考的话，那就是去看看upsetplot的代码。

GZZHY79 commented 1 year ago

好的，谢谢老师的回复，我还是本科生，本科也不是生信专业的，只是打算以后往这个方向发展，我会去收集一些资料，查阅文献，尝试去解决这个问题，再次感谢老师的指导。 --------------原始邮件-------------- 发件人："Guangchuang Yu @.>; 发送时间：2023年5月2日(星期二) 晚上11:40 收件人："YuLab-SMU/ProjectYulab" @.>; 抄送："耿宗依 @.>;"Mention @.>; 主题：Re: [YuLab-SMU/ProjectYulab] customize upset plot with aplot (Issue #3)

@GZZHY79 如果你是研究生的话，我想你应该清楚的。如果是本科生的话，那么提前体验。

如果比喻为学游泳，那就是直接扔水里，自己扑腾去吧。不要想着我学点什么，然后我就能干什么。趁早断了这念头。

要靠自己去探索，这个task，如果说有什么可以参考的话，那就是去看看upsetplot的代码。

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gaospecial commented 1 year ago

We can consider the upset plot as a composite plot, where each part can be drawn in the way that suits your needs, and then pieced together using aplot.

For example, the intersection part does not necessarily have to be drawn as the size of the intersection, it can be a feature of the intersection, such as the distribution of gene expression in the intersection. Of couse, for using aplot to create composite plots, you can also draw both the intersection size and feature together.

This is really a good idea, and I will try to do some work on this topic.

GuangchuangYu commented 1 year ago

see also https://github.com/cxli233/customized_upset_plots/blob/master/Scripts/customized_upset_plot_2023_01_19_read_data.Rmd, https://github.com/jokergoo/ComplexHeatmap_v2_paper_code/blob/master/figure5.R and ComplexHeatmap::UpSet().

GuangchuangYu commented 1 year ago

another useful package is https://github.com/ropensci/BaseSet, which provides useful utilities for set operations.