差異基因表達熱圖上有紅色和綠色的"官方"標準用法嗎?


1

我最近發現自己製作了多個熱圖,以可視化在兩個實驗條件下重複實驗之間的差異基因表達結果。

我使用顏色的繪圖軟件中的默認設置:

  • 基因上調->紅色
  • 基因下調->綠色
  • 不變的基因->黑色

我的直覺尖叫,我認為這種配色方案是相反的,上調的基因應該是綠色,而下調的基因應該是紅色。我問了幾個實驗室人員關於這種配色方案的直覺,並且發現在直觀上與每種不同方案相吻合的比例大約為50/50。

在該主題的搜索中,我發現several programs繪製的熱圖具有與我使用的程序相同的默認顏色(紅色=上調,綠色=下調)。另外,我在談話中被告知,這實質上是一個公認的標準。

如果這確實是慣例,我將開始嘗試重新連接我的直覺,但我想確認這是在我這樣做之前。但是,我還沒有找到代理商,發行商,現場主管部門等提供的"官方"指南,這些指南指定了熱圖中使用紅色/綠色。

我確實知道有很多suggestions for alternative heatmap color schemes,但是我有興趣為紅色/綠色方案找到一個正式的答案。

編輯:一些評論指出,沒有上述標準。因此,我將以下問題修改為:

是否有來自機構,發行商,該領域內機構等的"官方"指南,規定在熱圖中使用紅色/綠色?或相反,是否有任何"官方"準則說明沒有這樣的規範和/或任何這樣的顏色選擇是可以接受的?

1

Although there is no standard as DeepTools' Devon Ryan said, there are still some habits. Usually red means upregulated, as you can see in the default color scheme in MATLAB's clustergram function. But you also want to make sure color-blinded people can see the difference. So another color scheme might be better, such as red=high while blue=low. Anyway, if you can easily flip the color, using red to represent high is expected.


2

As others already pointed out, there is no official heatmap color scheme. I am not sure there is an official color scheme for any other types of plots either.

However, heatmaps seem to be far more standardized. Traditionally, heatmaps have been red-black-green as you originally stated. Most heatmaps from the microarray era and early RNA-seq are like that. You can have a heatmap for any type of data, but the majority is for gene expression. A lot of tools and tutorials were written back then, so they have that color scheme. From about 2008 to 2012, most people switched to the red-white-blue (or red-yellow-blue) color scheme. Switching green to blue avoids the color-blindness issue. Switching black to white is better for the ink if you print your papers and generally looks better on white background.

I originally found red as high to be confusing because I was thinking in financial terms (if the market is red, it's down). Now I think of it as a water faucet (red is hot, blue is cold).

Edit: In the last year or so, the viridis palette started to become widely used. It's far from the standard, but could become more popular in the future.