R:使用自动绘图时基于组的 PCA 中的颜色点
R: Color points in PCA based on groups when using autoplot
我制作了一个 PCA 图,其中我根据各种基因的表达绘制了许多细胞。在此图中,我想用单独的颜色为某些点着色。我试图通过创建 "groups" 来实现这一点,我在其中根据 "gene1" 的表达或缺乏表达对细胞进行排序。
这是我的数据框的样子(gene1、gene2 和 cell_1、cell_2 等是列名和行名):
gene1 gene2 gene3 gene4 gene5
cell_1 0.0000 0.279204 25.995400 46.171700 94.234100
cell_2 0.0000 23.456000 77.339800 194.241000 301.234000
cell_3 2.0000 13.100000 45.309200 0.776565 0.000000
cell_4 0.0000 10.500000 107.508000 3.032500 0.000000
cell_5 3.0000 0.000000 0.266139 0.762981 123.371000
这是我用来尝试实现此目的的代码:
library(ggplot2)
library(ggfortify)
# Group cells based on expression of a certain gene (to use for color labels in the next step)
groups <- factor(ifelse(df$gene1 > 0, "Positive", "Others"))
#Calculate PCs and plot PCA
autoplot(prcomp(log(df[]+1)), colour="Positive")
当我 运行 这段代码时,出现以下错误:
Error in grDevices::col2rgb(colour, TRUE) : invalid color name 'Positive'
这个怎么样?
df$groups <- factor(ifelse(df$gene1 > 0, "Positive", "Others"))
head(df)
gene1 gene2 gene3 gene4 gene5 groups
1 0.5638534 8.968558 94.40170 62.93106 290.442698 Positive
2 0.0000000 15.248374 45.87507 204.21703 291.501669 Others
3 1.9059518 19.488162 75.89302 97.69643 177.833347 Positive
4 1.9449987 6.358773 54.97159 41.54307 164.835188 Positive
5 0.0000000 16.568077 31.62370 23.72278 31.774541 Others
6 1.7199368 3.788276 80.51450 102.82221 6.259461 Positive
autoplot(prcomp(log(df[1:5]+1)), data=df, colour='groups')
我制作了一个 PCA 图,其中我根据各种基因的表达绘制了许多细胞。在此图中,我想用单独的颜色为某些点着色。我试图通过创建 "groups" 来实现这一点,我在其中根据 "gene1" 的表达或缺乏表达对细胞进行排序。
这是我的数据框的样子(gene1、gene2 和 cell_1、cell_2 等是列名和行名):
gene1 gene2 gene3 gene4 gene5
cell_1 0.0000 0.279204 25.995400 46.171700 94.234100
cell_2 0.0000 23.456000 77.339800 194.241000 301.234000
cell_3 2.0000 13.100000 45.309200 0.776565 0.000000
cell_4 0.0000 10.500000 107.508000 3.032500 0.000000
cell_5 3.0000 0.000000 0.266139 0.762981 123.371000
这是我用来尝试实现此目的的代码:
library(ggplot2)
library(ggfortify)
# Group cells based on expression of a certain gene (to use for color labels in the next step)
groups <- factor(ifelse(df$gene1 > 0, "Positive", "Others"))
#Calculate PCs and plot PCA
autoplot(prcomp(log(df[]+1)), colour="Positive")
当我 运行 这段代码时,出现以下错误:
Error in grDevices::col2rgb(colour, TRUE) : invalid color name 'Positive'
这个怎么样?
df$groups <- factor(ifelse(df$gene1 > 0, "Positive", "Others"))
head(df)
gene1 gene2 gene3 gene4 gene5 groups
1 0.5638534 8.968558 94.40170 62.93106 290.442698 Positive
2 0.0000000 15.248374 45.87507 204.21703 291.501669 Others
3 1.9059518 19.488162 75.89302 97.69643 177.833347 Positive
4 1.9449987 6.358773 54.97159 41.54307 164.835188 Positive
5 0.0000000 16.568077 31.62370 23.72278 31.774541 Others
6 1.7199368 3.788276 80.51450 102.82221 6.259461 Positive
autoplot(prcomp(log(df[1:5]+1)), data=df, colour='groups')