如何更改geom_dotplot中的形状并看到所有的点都在同一帧中？

Question

我想使用geom_dotplot通过点的形状和两个带有颜色的类别来区分两个不同的变量。例如，我有这个数据集：

Position    phaseGroup  phaseGroup_2    phaseGroup_3    Synonymous  Information Phasing Pha_Syn Grouped yPos
5.85E+04    1   1   1   16  1.1 Phased  Phased-16   1   1
5.96E+04    1   1   1   16  1.1 Phased  Phased-16   1   2
6.22E+04    1   1   1   16  1.1 Phased  Phased-16   1   3
6.26E+04    1   1   1   16  1.1 Phased  Phased-16   1   4
7.22E+04    NA  1   1   16  1.NA    Unphased    Unphased-16 1   5
7.30E+04    1   1   1   16  1.1 Phased  Phased-16   1   6
2.03E+05    2   2   2.1 16  1.2 Phased  Phased-16   1   7
2.48E+05    2   2   2.1 1   1.2 Phased  Phased-1    1   8
2.53E+05    2   2   2.1 16  1.2 Phased  Phased-16   1   9
2.53E+05    2   2   2.1 16  1.2 Phased  Phased-16   1   10
2.54E+05    2   2   2.1 16  1.2 Phased  Phased-16   1   11
2.54E+05    2   2   2.1 16  1.2 Phased  Phased-16   1   12
2.54E+05    NA  2   2.2 16  1.NA    Unphased    Unphased-16 1   13
2.55E+05    2   2   2.2 16  1.2 Phased  Phased-16   1   14
2.56E+05    2   2   2.2 16  1.2 Phased  Phased-16   1   15
2.58E+05    2   2   2.2 16  1.2 Phased  Phased-16   1   16
2.61E+05    2   2   2.2 16  1.2 Phased  Phased-16   1   17
5.76E+05    3   3   3.1 16  1.3 Phased  Phased-16   1   18
5.77E+05    3   3   3.1 16  1.3 Phased  Phased-16   1   19
5.77E+05    3   3   3.1 16  1.3 Phased  Phased-16   1   20
5.79E+05    3   3   3.1 16  1.3 Phased  Phased-16   1   21
6.22E+05    3   3   3.1 16  1.3 Phased  Phased-16   1   22
6.23E+05    3   3   3.1 1   1.3 Phased  Phased-1    1   23
6.24E+05    3   3   3.2 16  1.3 Phased  Phased-16   1   24
6.25E+05    3   3   3.2 16  1.3 Phased  Phased-16   1   25
6.26E+05    3   3   3.2 16  1.3 Phased  Phased-16   1   26
6.27E+05    3   3   3.2 16  1.3 Phased  Phased-16   1   27
6.29E+05    3   3   3.2 16  1.3 Phased  Phased-16   1   28
6.29E+05    3   3   3.2 16  1.3 Phased  Phased-16   1   29
6.31E+05    3   3   3.3 16  1.3 Phased  Phased-16   1   30
6.32E+05    3   3   3.3 16  1.3 Phased  Phased-16   1   31
6.32E+05    3   3   3.3 16  1.3 Phased  Phased-16   1   32
6.34E+05    3   3   3.3 16  1.3 Phased  Phased-16   1   33
6.35E+05    3   3   3.3 16  1.3 Phased  Phased-16   1   34
6.37E+05    3   3   3.3 16  1.3 Phased  Phased-16   1   35
6.76E+05    3   3   3.4 16  1.3 Phased  Phased-16   1   36
6.82E+05    3   3   3.4 16  1.3 Phased  Phased-16   1   37
7.40E+05    3   3   3.4 16  1.3 Phased  Phased-16   1   38
7.57E+05    3   3   3.4 16  1.3 Phased  Phased-16   1   39
7.60E+05    3   3   3.4 16  1.3 Phased  Phased-16   1   40
7.61E+05    3   3   3.4 16  1.3 Phased  Phased-16   1   41
7.61E+05    3.5 3.5 3.5 16  2.1 Phased  Phased-16   2   41.5
2.03E+06    4   4   4   16  3.4 Phased  Phased-16   3   42
2.10E+06    4   4   4   1   3.4 Phased  Phased-1    3   43
2.15E+06    4   4   4   16  3.4 Phased  Phased-16   3   44
2.16E+06    4   4   4   16  3.4 Phased  Phased-16   3   45
2.16E+06    4   4   4   16  3.4 Phased  Phased-16   3   46
2.16E+06    4   4   4   16  3.4 Phased  Phased-16   3   47
2.17E+06    4   4   4   1   3.4 Phased  Phased-1    3   48
2.18E+06    NA  4   4   1   3.NA    Unphased    Unphased-1  3   49
2.36E+06    5   5   5   16  3.5 Phased  Phased-16   3   50
2.36E+06    5   5   5   16  3.5 Phased  Phased-16   3   51
2.37E+06    5   5   5   16  3.5 Phased  Phased-16   3   52
2.37E+06    5   5   5   1   3.5 Phased  Phased-1    3   53
2.37E+06    5   5   5   1   3.5 Phased  Phased-1    3   54
2.37E+06    5   5   5   16  3.5 Phased  Phased-16   3   55
2.37E+06    5   5   5   16  3.5 Phased  Phased-16   3   56
2.37E+06    5   5   5   1   3.5 Phased  Phased-1    3   57
2.50E+06    5   5   5   16  3.5 Phased  Phased-16   3   58
2.50E+06    5   5   5   16  3.5 Phased  Phased-16   3   59
2.53E+06    5   5   5   1   3.5 Phased  Phased-1    3   60
2.54E+06    5   5   5   16  3.5 Phased  Phased-16   3   61
2.54E+06    5   5   5   1   3.5 Phased  Phased-1    3   62
2.56E+06    5   5   5   16  3.5 Phased  Phased-16   3   63
2.60E+06    5   5   5   16  3.5 Phased  Phased-16   3   64
2.62E+06    5   5   5   16  3.5 Phased  Phased-16   3   65
3.04E+06    NA  5   5   1   4.NA    Unphased    Unphased-1  4   66
3.17E+06    NA  5   5   1   4.NA    Unphased    Unphased-1  4   67
3.84E+06    NA  5   5   16  4.NA    Unphased    Unphased-16 4   68
4.00E+06    6   6   6   16  5.6 Phased  Phased-16   5   69
4.00E+06    6   6   6   16  5.6 Phased  Phased-16   5   70
4.00E+06    6   6   6   16  5.6 Phased  Phased-16   5   71
4.00E+06    6   6   6   1   5.6 Phased  Phased-1    5   72
4.00E+06    6   6   6   16  5.6 Phased  Phased-16   5   73
4.00E+06    NA  6   6   16  5.NA    Unphased    Unphased-16 5   74
4.00E+06    NA  6   6   16  5.NA    Unphased    Unphased-16 5   75
4.00E+06    7   7   7   16  5.7 Phased  Phased-16   5   76
4.00E+06    7   7   7   16  5.7 Phased  Phased-16   5   77
4.00E+06    7   7   7   1   5.7 Phased  Phased-1    5   78
4.00E+06    7   7   7   1   5.7 Phased  Phased-1    5   79
4.00E+06    7   7   7   16  5.7 Phased  Phased-16   5   80
4.00E+06    7   7   7   16  5.7 Phased  Phased-16   5   81
4.00E+06    8   8   8   16  5.8 Phased  Phased-16   5   82
4.00E+06    8   8   8   16  5.8 Phased  Phased-16   5   83
4.00E+06    8   8   8   16  5.8 Phased  Phased-16   5   84
4.00E+06    8   8   8   16  5.8 Phased  Phased-16   5   85
4.00E+06    8   8   8   16  5.8 Phased  Phased-16   5   86
4.00E+06    8   8   8   16  5.8 Phased  Phased-16   5   87
4.00E+06    8   8   8   16  5.8 Phased  Phased-16   5   88
4.00E+06    8   8   8   16  5.8 Phased  Phased-16   5   89
4.00E+06    8   8   8   16  5.8 Phased  Phased-16   5   90
4.00E+06    8   8   8   16  5.8 Phased  Phased-16   5   91
4.00E+06    8   8   8   16  5.8 Phased  Phased-16   5   92
4.00E+06    8   8   8   16  5.8 Phased  Phased-16   5   93
4.00E+06    8   8   8   16  5.8 Phased  Phased-16   5   94
4.00E+06    8   8   8   16  5.8 Phased  Phased-16   5   95
4.00E+06    8   8   8   16  5.8 Phased  Phased-16   5   96
4.00E+06    8   8   8   16  5.8 Phased  Phased-16   5   97
4.00E+06    8   8   8   16  5.8 Phased  Phased-16   5   98
4.00E+06    8   8   8   16  5.8 Phased  Phased-16   5   99
4.00E+06    8   8   8   16  5.8 Phased  Phased-16   5   100
4.00E+06    8   8   8   16  5.8 Phased  Phased-16   5   101
4.01E+06    8   8   8   16  5.8 Phased  Phased-16   5   102
4.01E+06    8   8   8   16  5.8 Phased  Phased-16   5   103
4.01E+06    9   9   9   16  5.9 Phased  Phased-16   5   104
4.01E+06    9   9   9   16  5.9 Phased  Phased-16   5   105
4.01E+06    NA  9   9   16  5.NA    Unphased    Unphased-16 5   106
4.01E+06    9   9   9   16  5.9 Phased  Phased-16   5   107
4.01E+06    9   9   9   16  5.9 Phased  Phased-16   5   108
4.01E+06    9   9   9   16  5.9 Phased  Phased-16   5   109
4.01E+06    9   9   9   16  5.9 Phased  Phased-16   5   110
4.01E+06    9   9   9   16  5.9 Phased  Phased-16   5   111
4.01E+06    9   9   9   16  5.9 Phased  Phased-16   5   112
4.01E+06    9   9   9   16  5.9 Phased  Phased-16   5   113
4.01E+06    9   9   9   16  5.9 Phased  Phased-16   5   114
4.01E+06    9   9   9   16  5.9 Phased  Phased-16   5   115
4.01E+06    9   9   9   16  5.9 Phased  Phased-16   5   116
4.01E+06    9   9   9   16  5.9 Phased  Phased-16   5   117
4.01E+06    9   9   9   16  5.9 Phased  Phased-16   5   118
4.01E+06    NA  9   9   1   5.NA    Unphased    Unphased-1  5   119
4.02E+06    9   9   9   16  5.9 Phased  Phased-16   5   120
4.02E+06    10  10  10  1   5.1 Phased  Phased-1    5   121
4.02E+06    10  10  10  16  5.1 Phased  Phased-16   5   122
4.02E+06    NA  10  10  1   5.NA    Unphased    Unphased-1  5   123
4.02E+06    10  10  10  16  5.1 Phased  Phased-16   5   124
4.02E+06    10  10  10  16  5.1 Phased  Phased-16   5   125
4.02E+06    10  10  10  1   5.1 Phased  Phased-1    5   126
4.02E+06    10  10  10  1   5.1 Phased  Phased-1    5   127
4.02E+06    10  10  10  1   5.1 Phased  Phased-1    5   128
4.02E+06    NA  10  10  1   5.NA    Unphased    Unphased-1  5   129
4.02E+06    10  10  10  1   5.1 Phased  Phased-1    5   130
4.02E+06    10  10  10  1   5.1 Phased  Phased-1    5   131
4.02E+06    10  10  10  16  5.1 Phased  Phased-16   5   132
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   133
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   134
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   135
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   136
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   137
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   138
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   139
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   140
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   141
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   142
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   143
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   144
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   145
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   146
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   147
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   148
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   149
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   150
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   151
4.03E+06    NA  10  10  16  5.NA    Phased  Phased-16   5   152
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   153
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   154
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   155
4.03E+06    10  10  10  16  5.1 Phased  Phased-16   5   156
4.04E+06    10  10  10  16  5.1 Phased  Phased-16   5   157
4.04E+06    10  10  10  1   5.1 Phased  Phased-1    5   158
4.04E+06    10  10  10  1   5.1 Phased  Phased-1    5   159
4.04E+06    10  10  10  1   5.1 Phased  Phased-1    5   160
4.04E+06    10  10  10  16  5.1 Phased  Phased-16   5   161
4.04E+06    10  10  10  16  5.1 Phased  Phased-16   5   162
4.04E+06    NA  10  10  16  5.NA    Unphased    Unphased-16 5   163
4.04E+06    NA  10  10  16  5.NA    Unphased    Unphased-16 5   164
4.04E+06    10  10  10  16  5.1 Phased  Phased-16   5   165
4.04E+06    NA  10  10  16  5.NA    Unphased    Unphased-16 5   166
4.04E+06    10  10  10  16  5.1 Phased  Phased-16   5   167
4.04E+06    10  10  10  1   5.1 Phased  Phased-1    5   168
4.04E+06    10  10  10  1   5.1 Phased  Phased-1    5   169
4.04E+06    10  10  10  1   5.1 Phased  Phased-1    5   170
4.04E+06    10  10  10  16  5.1 Phased  Phased-16   5   171
4.04E+06    10  10  10  1   5.1 Phased  Phased-1    5   172
4.04E+06    NA  10  10  16  5.NA    Unphased    Unphased-16 5   173
4.04E+06    10  10  10  16  5.1 Phased  Phased-16   5   174
4.04E+06    10  10  10  16  5.1 Phased  Phased-16   5   175
4.04E+06    NA  10  10  16  5.NA    Unphased    Unphased-16 5   176
4.04E+06    10  10  10  16  5.1 Phased  Phased-16   5   177
4.04E+06    10  10  10  1   5.1 Phased  Phased-1    5   178
4.04E+06    10  10  10  1   5.1 Phased  Phased-1    5   179
4.04E+06    10  10  10  16  5.1 Phased  Phased-16   5   180
4.04E+06    10  10  10  16  5.1 Phased  Phased-16   5   181
4.04E+06    10  10  10  1   5.1 Phased  Phased-1    5   182
4.04E+06    10  10  10  16  5.1 Phased  Phased-16   5   183
4.04E+06    10  10  10  16  5.1 Phased  Phased-16   5   184
4.04E+06    10  10  10  16  5.1 Phased  Phased-16   5   185
4.04E+06    NA  10  10  16  5.NA    Unphased    Unphased-16 5   186
4.04E+06    10  10  10  16  5.1 Phased  Phased-16   5   187
4.05E+06    10  10  10  16  5.1 Phased  Phased-16   5   188
4.05E+06    10  10  10  16  5.1 Phased  Phased-16   5   189
4.05E+06    10  10  10  16  5.1 Phased  Phased-16   5   190
4.05E+06    10  10  10  1   5.1 Phased  Phased-1    5   191
4.05E+06    10  10  10  16  5.1 Phased  Phased-16   5   192
4.05E+06    10  10  10  16  5.1 Phased  Phased-16   5   193
4.05E+06    10  10  10  16  5.1 Phased  Phased-16   5   194
4.05E+06    10  10  10  16  5.1 Phased  Phased-16   5   195
4.05E+06    10  10  10  1   5.1 Phased  Phased-1    5   196
4.05E+06    10  10  10  1   5.1 Phased  Phased-1    5   197
4.05E+06    10  10  10  1   5.1 Phased  Phased-1    5   198
4.05E+06    10  10  10  1   5.1 Phased  Phased-1    5   199
4.05E+06    10  10  10  1   5.1 Phased  Phased-1    5   200
4.05E+06    10  10  10  1   5.1 Phased  Phased-1    5   201
4.05E+06    10  10  10  1   5.1 Phased  Phased-1    5   202
4.05E+06    10  10  10  1   5.1 Phased  Phased-1    5   203
4.05E+06    10  10  10  1   5.1 Phased  Phased-1    5   204
4.05E+06    10  10  10  16  5.1 Phased  Phased-16   5   205
4.05E+06    10  10  10  1   5.1 Phased  Phased-1    5   206
4.05E+06    10  10  10  1   5.1 Phased  Phased-1    5   207
4.05E+06    10  10  10  1   5.1 Phased  Phased-1    5   208
4.59E+06    NA  10  10  16  5.NA    Unphased    Unphased-16 5   209

我运行以下命令行：

library(ggplot2)
ggplot(A, aes(x = factor(Grouped), y = phaseGroup_2, fill = factor(Phasing))) + 
  geom_dotplot(binaxis="y",stackdir = "center", dotsize = 0.3) + 
  theme_minimal()

并生成了附件中的图形。

但是，我想在此图中做两件事，因为您可以看到y = 10处的第5组，我看不到所有点，但是如果我将点缩小，则看不到颜色。其次，我想根据Synonymous列更改图形的形状（1-实心圆和16-实心圆）。

我的问题是如何改变点的形状并以可以看到所有点的方式优化图形？重要说明是，我想保持水平数据的数量相同，这意味着，正如您在第1组中看到的那样，我有3个水平数据点，而在第2组中只有一个。

有什么方法可以优化这个数字，我是否需要在ggplot中尝试另一个命令行？

Answer 1

你能做这样的事吗？

library(tidyverse)

df <-
  A %>% 
  mutate(y = ifelse(Grouped == 4, phaseGroup_2 + 0.2, phaseGroup_2))

ggplot(df) +
  geom_dotplot(
    aes(x = Grouped, y = y, group = Grouped, fill = factor(Phasing))
    binaxis = "y",
    stackdir = "center",
    dotsize = 0.6
  ) +
  scale_x_continuous(breaks = c(1:5), limits = c(-6, 16)) +
  theme(
    panel.grid.minor = element_blank(),
    panel.grid.major.y = element_blank()
  )

我注意到phaseGroup_2 == 4时，您有2个小组并排放置，所以我将该小组撞了一些。

此外，请将来将您的数据集作为代码提供给我们。 datapasta软件包有一个很好的加载项，可以将剪贴板上的某些内容从excel粘贴到tribble或data.frame。 https://reprex.tidyverse.org/articles/articles/datapasta-reprex.html

Answer 2

如果我理解正确，则OP正在寻找多个类别数据的可视化文件。 OP尝试使用ggplot2::geom_dotplot()来可视化4类phaseGroup_2，Grouped，Phasing和Synonymous的计数。

此答案试图探索不同的方法：

1. geom_dotplot()的解决方法
2. ggbeeswarm
3. vcd和ggmosaic

使用geom_dotplot()的{​​{1}}的解决方法

正如mentioned by aosmith一样，interaction()并没有意识到geom_dotplot()的美感。相反，对于OP要求的小点尺寸，使用shape或colour美观度并不能给出很好的可分辨结果。

一种解决方法是将alpha和colour的美感用于变量fill和Phasing的组合（交互）。这两个变量都是二分的。因此，仅需要4种不同的颜色。

Synonymous

library(ggplot2) ggplot(A) + aes(x = factor(Grouped), y = phaseGroup_2, colour = interaction(Phasing, Synonymous), fill = interaction(Phasing, Synonymous)) + geom_dotplot(binaxis = "y", stackdir = "center", dotsize = 0.3) + scale_y_continuous(breaks = unique(A$phaseGroup_2), minor_breaks = NULL) + scale_colour_brewer(palette = "RdBu", direction = -1, aesthetics = c("colour", "fill")) + expand_limits(x = 6) + theme_minimal() 使用实心圆，如果仅使用geom_dotplot()美学，则该实心圆在每个点周围绘制黑色轮廓。为了提高感知度，fill和colour使用相同的编码。

但是，并非所有点都是完全可见的，因为有些点由于过度绘图而在其他点之后被掩盖。特别是，fill情况下的蓝色点几乎不可见。

顺便说一句，可以直接使用OP数据集中的等效列Synonymous == 1代替interaction(Phasing, Synonymous)。

进一步的改进包括：

• 扩展x轴以防止Pha_Syn中的点被切除（按照OP的要求）。
• 将y轴绘制为连续变量，以便可见3、3.5和4之间的非等距距离。

Grouped == 5

ggbeeswarm了解与geom_beeswarm()相同的美学，包括geom_point()美学。此外，它避免了过度绘图。

shape

可以清楚地区分空心和实心圆。

library(ggbeeswarm) ggplot(A) + aes(x = Grouped, y = phaseGroup_2, colour = Phasing, shape = Synonymous) + geom_beeswarm() + scale_x_continuous(breaks = unique(A$Grouped), minor_breaks = NULL) + scale_y_continuous(breaks = unique(A$phaseGroup_2), minor_breaks = NULL) + scale_shape_identity() + theme_minimal() 和vcd

ggmosaic程序包包含许多用于可视化分类数据的图。我尝试使用vcd包中的mosaic()，doubledecker()和tile()（以及{{1 }}程序包），但不幸的是，由于存在大量的空单元，它们都没有给出令人满意的结果。

可复制的数据

vcd软件包中的ggplot2函数能够读取OP的数据，而无需额外的人工干预。

ggmosaic