如何使用大矩阵制作热图? [英] How can I make a heatmap with a large matrix?

问题描述

我有一个1000 * 1000的矩阵(仅包含整数0和1)，但是当我尝试制作热图时，会发生错误，因为它太大了.

I have a 1000*1000 matrix (which only includes integer 0 and 1), but when I tried to make a heatmap, an error occurs because it is too large.

如何使用如此大的矩阵创建热图?

How can I create a heatmap with such a large matrix?

推荐答案

我可以相信，热图至少需要花费很长时间，因为heatmap做了很多花哨的东西，这需要额外的时间和内存.使用@ bill_080的示例中的dat:

I can believe that the heatmap is, at least, taking a long time, because heatmap does a lot of fancy stuff that takes extra time and memory. Using dat from @bill_080's example:

## basic command: 66 seconds
t0 <- system.time(heatmap(dat))
## don't reorder rows & columns: 43 seconds
t1 <- system.time(heatmap(dat,Rowv=NA))
## remove most fancy stuff (from ?heatmap): 14 seconds
t2 <- system.time( heatmap(dat, Rowv = NA, Colv = NA, scale="column",
             main = "heatmap(*, NA, NA) ~= image(t(x))"))
## image only: 13 seconds
t3  <- system.time(image(dat))
## image using raster capability in R 2.13.0: 1.2 seconds
t4 <- system.time(image(dat,useRaster=TRUE))

您可能要考虑热图中真正想要的东西-即，您是否需要精美的树状图/重新排序的东西?

You might want to consider what you really want out of the heatmap -- i.e., do you need the fancy dendrogram/reordering stuff?

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