如何解决在 Factoextra 上改变形状
我是一名非常新的编码员，希望改变我的 PCA Biplot 的形状。我的 PCA Biplot 代码如下：
group <- c(rep("SHIME 1_Trt1",times=8),rep('SHIME 1_Trt2',times=6),rep("SHIME 2_Trt1",rep('SHIME 2_Trt2',rep("SHIME 3_Trt1",rep('SHIME 3_Trt2',times=6))
clusters <- c(rep("SCFA",times=3),rep("Organic acid",rep("Alcohols",rep('AA',times=2),rep('Ketone',times=1),rep('Lipid',times=1))
j_scale <- prcomp(j,center=TRUE,scale=TRUE)
fviz_pca_biplot(j_scale,repel=TRUE,pointsize=4,pointshape=21,col.var=factor(clusters),arrowsize=0.6,labelsize=4,palette=c("#00AFBB","#00AFBB","#E7B800","#FC4E07","#FC4E08"),geom='point',fill.ind=group,legend.title=list(fill='System',color='Categories')) +
ggpubr::color_palette("lancet")
颜色按我喜欢的方式排列，但我希望Trts之间的形状不同。 示例：shime1 trt 1 = 蓝色圆圈、shime 1 trt 2 = 蓝色正方形、shime 2 trt 1 = 绿色圆圈等。请参见下图了解当前双标图。
我试过了：
scale_shape_manual(values=c()),habillage=group #doesn't give me the same output as fill.ind and clashes with col.var=,geom.ind/var,and shape.ind
Changing pointshape=c() doesn't seem to work either
fviz_pca_biplot(j_scale,col.ind=shimeb_pca$Type,col.var='black',legend.title=list(fill='System')) + theme_minimal() +
scale_shape_manual(values=c(5,20,21,20))
#This looks worse than the original code
prcomp(j,scale=TRUE) 之前的数据摘录：
Acetate Propionate Butyrate Lactate Formate Succinate Ethanol Methanol
S1_0 40.09358 10.726725 0.7180000 0.6104750 1.901075 0.5284000 10.730900 1.163525
S1_1 40.05890 10.962025 0.6841500 0.7253000 1.958825 0.7286250 11.013750 1.217125
S1_1.5 44.27740 13.020812 0.8308875 0.4131125 1.355225 0.0539250 10.897100 1.267700
S1_2 43.87610 11.580800 0.6531500 0.7476500 2.461150 0.7961250 9.628950 1.338500
S1_3 45.70235 12.458150 0.7131750 0.4026250 2.059375 0.5043250 20.098575 1.426900
S1_5 45.15580 12.711575 0.7775750 0.1914750 0.864700 0.0535750 10.404050 1.357200
S1_7 44.11000 12.885625 0.7210250 0.3525500 2.534225 0.0616750 7.744150 1.431675
S1_9 47.27562 12.739375 0.6837000 0.4053000 2.804775 0.0570500 13.701000 1.630200
感谢任何帮助。提前致谢。
解决方法
试试fviz_pca_biplot(j_scale,geom.ind = 'point',repel = TRUE,pointsize = 4,habillage = group,arrowsize = 0.6,labelsize = 4,legend.title = list(fill = 'System'))
干得好。
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