R：哪个热图/图像在没有任何树状图的情况下获得行排序图？ [英] R: Which heatmap/image to get row-sorted plot without any dendrogram?

问题描述

哪个包最适合热图/图像，仅对行进行排序，但不显示任何树形图或其他视觉混乱（只是在两个轴上都带有自动命名标签的2D彩色网格） 。除了基本的数字排序之外，我不需要花哨的聚类。数据是一个39x10的数字表，范围（0,0.21）我想要可视化。

Which package is best for a heatmap/image with sorting on rows only, but don't show any dendrogram or other visual clutter (just a 2D colored grid with automatic named labels on both axes). I don't need fancy clustering beyond basic numeric sorting. The data is a 39x10 table of numerics in the range (0,0.21) which I want to visualize.

我搜索了SO（参见这个）和R网站，并尝试了几个。查看 R图形手册以查看出色的可搜索性屏幕截图列表和相应的软件包。

I searched SO (see this) and the R sites, and tried a few out. Check out R Graphical Manual to see an excellent searchable list of screenshots and corresponding packages.

软件包的范围令人困惑 - 哪一个是首选热图（如 ggplot2 适用于大多数其他绘图）？这是我到目前为止所发现的：

The range of packages is confusing - which one is the preferred heatmap (like ggplot2 is for most other plotting)? Here is what I found out so far:

• base ::图像 - 错误，轴上没有名称标签，没有排序/聚类


• base :: heatmap - 选项比以下内容更难理解：


• pheatmap :: pheatmap - 很棒，但似乎无法关闭
  树状图？ （任何黑客？）


• ggplot2人使用geom_tile，正如Andrie指出的那样


• gplots :: heatmap.2 ， ref - 似乎是b b b受到生物技术人士的青睐，但对于我的目的来说却是过度杀戮。 （与 ggplot * 或Wickham教授没有
  的关系）


• plotrix :: color2D.matplot 也存在

• base::image - bad, no name labels on axes, no sorting/clustering
• base::heatmap - options are far less intelligible than the following:
• pheatmap::pheatmap - fantastic but can't seem to turn off the dendrograms? (any hacks?)
• ggplot2 people use geom_tile, as Andrie points out
• gplots::heatmap.2 , ref - seems to be favored by biotech people, but way overkill for my purposes. (no relation to ggplot* or Prof Wickham)
• plotrix::color2D.matplot also exists

base :: heatmap 很烦人，即使使用args heatmap（ ...，Colv = NA，keep.dendro = FALSE） 它仍然在行上绘制不需要的树形图。

base::heatmap is annoying, even with args heatmap(..., Colv=NA, keep.dendro=FALSE) it still plots the unwanted dendrogram on rows.

For现在我要用 pheatmap（...，cluster_cols = FALSE，cluster_rows = FALSE） 并手动预先分配我的表，就像这个人一样： 热图中的行数排序？

For now I'm going with pheatmap(..., cluster_cols=FALSE, cluster_rows=FALSE) and manually presorting my table, like this guy: Order of rows in heatmap?

附录：要显示每个单元格内的值，请参阅：显示矩阵，包括值，作为热图。我不需要那个，但它很不错。

Addendum: to display the value inside each cell, see: display a matrix, including the values, as a heatmap . I didn't need that but it's nice-to-have.

推荐答案

使用 pheatmap 你可以使用选项 treeheight_row 和 treeheight_col 并将它们设置为0.

With pheatmap you can use options treeheight_row and treeheight_col and set these to 0.

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