我不清楚样本名称是否是数据框中的行名称，所以我只是重新创建了数据框，将样本名称放入一个变量中，就像细菌名称一样：

Sample Actinobacteria Bacteroidetes Firmicutes Fusobacteria Proteobacteria
1 sample1    0.008424628     0.4162710  0.5547550 0.000000e+00   0.0007245180
2 sample2    0.016857133     0.1329880  0.8028944 3.560112e-05   0.0042721350
3 sample3    0.002029929     0.5381382  0.4236795 3.311006e-02   0.0007978327
  Verrucomicrobia       Other
1    5.391762e-05 0.019770920
2    4.238314e-02 0.000569618
3    3.534702e-05 0.002209189

要重新生成此数据集，可以运行以下命令：

df <- structure(list(Sample = structure(1:3, .Label = c("sample1", 
"sample2", "sample3"), class = "factor"), Actinobacteria = c(0.0084246282, 
0.0168571327, 0.0020299288), Bacteroidetes = c(0.41627099, 0.132988, 
0.53813817), Firmicutes = c(0.55475503, 0.80289437, 0.42367947
), Fusobacteria = c(0, 3.560112e-05, 0.03311006), Proteobacteria = c(0.000724518, 
0.004272135, 0.0007978327), Verrucomicrobia = c(5.391762e-05, 
0.04238314, 3.534702e-05), Other = c(0.01977092, 0.000569618, 
0.002209189)), .Names = c("Sample", "Actinobacteria", "Bacteroidetes", 
"Firmicutes", "Fusobacteria", "Proteobacteria", "Verrucomicrobia", 
"Other"), class = "data.frame", row.names = c("1", "2", "3"))

正如@zx8754所建议的，此 Dataframe 需要重新整形，即从宽格式移动到长格式。有关详细信息，请查看此link中的一些示例。
如果上面的 Dataframe 命名为df，则以下命令将以长格式对其进行整形：

library(reshape2)
df_long <- melt(df, id.vars = "Sample", variable.name = "Phyla")

从这里我们可以使用ggplot绘图：

library(ggplot2)
ggplot(df_long, aes(x = Sample, y = value, fill = Phyla)) + 
    geom_bar(stat = "identity")

其给出：