我正在使用R清理STRUCTURE图(Wilson和Rannala,2003)。该程序生成的绘图本身是可以的,但是我正在生成多个绘图,并希望保持多个因素一致,以便于读者阅读。原始地块的标签和组是按总体而不是按个人划分的,例如:(https://i.imgur.com/MAwJoEP.png)
这些是我正在使用的数据:
Group Ind pop_est K
UD MAUD13 0.003 P1
UD MAUD14 0.004 P1
UD MAUD15 0.003 P1
UD MAUD16 0.005 P1
UD MAUD17 0.025 P1
UD MAUD18 0.007 P1
UD MAUD19 0.01 P1
UD MAUD21 0.003 P1
UD MAUD23 0.013 P1
MD MAMD1 0.013 P1
MD MAMD2 0.015 P1
MD MAMD3 0.007 P1
MD MAMD4 0.009 P1
MD MAMD5 0.004 P1
MD MAMD6 0.004 P1
MD MAMD7 0.003 P1
LD MALD1 0.015 P1
LD MALD2 0.003 P1
LD MALD3 0.007 P1
LD MALD4 0.01 P1
LD MALD5 0.004 P1
LD MALD6 0.004 P1
LD MALD7 0.026 P1
LD MALD8 0.009 P1
LD MALD9 0.006 P1
LD MALD10 0.003 P1
LD MALD12 0.005 P1
LD MALD13 0.008 P1
LD MALD14 0.004 P1
LD MALD15 0.01 P1
LD MALD16 0.004 P1
LD MALD17 0.028 P1
LD MALD18 0.004 P1
LD MALD19 0.008 P1
LD MALD20 0.003 P1
LD MALD21 0.004 P1
LD MALD23 0.018 P1
LD MALD24 0.006 P1
LD MALD25 0.003 P1
LD MALD26 0.006 P1
LD MALD27 0.006 P1
LD MALD28 0.006 P1
LD MALD29 0.004 P1
LD MALD30 0.005 P1
UM MAUM1 0.991 P1
UM MAUM2 0.987 P1
UM MAUM3 0.988 P1
UM MAUM4 0.986 P1
UM MAUM5 0.983 P1
UM MAUM6 0.993 P1
UM MAUM7 0.979 P1
UM MAUM8 0.991 P1
UM MAUM9 0.991 P1
UM MAUM10 0.988 P1
UM MAUM11 0.993 P1
UM MAUM12 0.985 P1
UM MAUM13 0.99 P1
UM MAUM14 0.992 P1
UM MAUM15 0.994 P1
UM MAUM16 0.978 P1
UM MAUM17 0.991 P1
UM MAUM18 0.99 P1
UM MAUM19 0.991 P1
UM MAUM20 0.99 P1
MM MAMM1 0.986 P1
MM MAMM2 0.991 P1
MM MAMM3 0.993 P1
MM MAMM4 0.959 P1
MM MAMM5 0.987 P1
MM MAMM6 0.982 P1
MM MAMM7 0.993 P1
MM MAMM8 0.993 P1
MM MAMM9 0.993 P1
MM MAMM10 0.991 P1
MM MAMM11 0.993 P1
MM MAMM12 0.982 P1
MM MAMM13 0.989 P1
MM MAMM14 0.991 P1
MM MAMM15 0.993 P1
MM MAMM16 0.993 P1
MM MAMM17 0.989 P1
MM MAMM18 0.992 P1
MM MAMM19 0.992 P1
MM MAMM20 0.974 P1
LM MALM1 0.004 P1
LM MALM2 0.003 P1
LM MALM3 0.006 P1
LM MALM4 0.003 P1
LM MALM5 0.004 P1
LM MALM6 0.004 P1
LM MALM7 0.003 P1
LM MALM8 0.003 P1
LM MALM9 0.003 P1
LM MALM10 0.003 P1
LM MALM11 0.004 P1
LM MALM12 0.004 P1
LM MALM13 0.02 P1
LM MALM14 0.003 P1
LM MALM15 0.003 P1
LM MALM16 0.003 P1
LM MALM17 0.004 P1
LM MALM18 0.005 P1
LM MALM19 0.01 P1
LM MALM20 0.004 P1
UK MAUK1 0.003 P1
UK MAUK2 0.005 P1
UK MAUK3 0.003 P1
UK MAUK4 0.003 P1
UK MAUK5 0.004 P1
UK MAUK6 0.004 P1
UK MAUK7 0.004 P1
UK MAUK8 0.044 P1
UK MAUK9 0.005 P1
UK MAUK10 0.003 P1
UK MAUK11 0.007 P1
UK MAUK12 0.004 P1
UK MAUK13 0.004 P1
UK MAUK14 0.004 P1
UK MAUK15 0.003 P1
UK MAUK16 0.005 P1
UK MAUK17 0.017 P1
UK MAUK18 0.004 P1
UK MAUK19 0.007 P1
UK MAUK20 0.007 P1
MK MAMK1 0.006 P1
MK MAMK2 0.005 P1
MK MAMK3 0.023 P1
MK MAMK4 0.009 P1
MK MAMK5 0.007 P1
MK MAMK6 0.008 P1
MK MAMK7 0.004 P1
MK MAMK8 0.015 P1
MK MAMK9 0.005 P1
MK MAMK10 0.011 P1
MK MAMK11 0.004 P1
MK MAMK12 0.004 P1
MK MAMK13 0.019 P1
MK MAMK14 0.004 P1
MK MAMK15 0.008 P1
MK MAMK16 0.003 P1
MK MAMK17 0.003 P1
MK MAMK18 0.012 P1
MK MAMK19 0.006 P1
MK MAMK20 0.006 P1
LK MALK1 0.009 P1
LK MALK2 0.011 P1
LK MALK3 0.004 P1
LK MALK4 0.01 P1
LK MALK5 0.022 P1
LK MALK6 0.063 P1
LK MALK7 0.081 P1
LK MALK8 0.003 P1
LK MALK9 0.005 P1
LK MALK10 0.068 P1
LK MALK11 0.003 P1
LK MALK12 0.004 P1
LK MALK13 0.004 P1
LK MALK14 0.008 P1
LK MALK15 0.006 P1
LK MALK16 0.007 P1
LK MALK17 0.011 P1
LK MALK18 0.005 P1
LK MALK19 0.007 P1
LK MALK21 0.004 P1
UD MAUD13 0.991 P2
UD MAUD14 0.991 P2
UD MAUD15 0.991 P2
UD MAUD16 0.987 P2
UD MAUD17 0.967 P2
UD MAUD18 0.945 P2
UD MAUD19 0.949 P2
UD MAUD21 0.991 P2
UD MAUD23 0.971 P2
MD MAMD1 0.976 P2
MD MAMD2 0.961 P2
MD MAMD3 0.988 P2
MD MAMD4 0.968 P2
MD MAMD5 0.97 P2
MD MAMD6 0.991 P2
MD MAMD7 0.985 P2
LD MALD1 0.967 P2
LD MALD2 0.992 P2
LD MALD3 0.984 P2
LD MALD4 0.975 P2
LD MALD5 0.97 P2
LD MALD6 0.982 P2
LD MALD7 0.969 P2
LD MALD8 0.94 P2
LD MALD9 0.981 P2
LD MALD10 0.99 P2
LD MALD12 0.951 P2
LD MALD13 0.987 P2
LD MALD14 0.986 P2
LD MALD15 0.981 P2
LD MALD16 0.991 P2
LD MALD17 0.922 P2
LD MALD18 0.991 P2
LD MALD19 0.984 P2
LD MALD20 0.992 P2
LD MALD21 0.986 P2
LD MALD23 0.979 P2
LD MALD24 0.987 P2
LD MALD25 0.989 P2
LD MALD26 0.982 P2
LD MALD27 0.988 P2
LD MALD28 0.99 P2
LD MALD29 0.992 P2
LD MALD30 0.986 P2
UM MAUM1 0.006 P2
UM MAUM2 0.005 P2
UM MAUM3 0.003 P2
UM MAUM4 0.004 P2
UM MAUM5 0.01 P2
UM MAUM6 0.004 P2
UM MAUM7 0.014 P2
UM MAUM8 0.004 P2
UM MAUM9 0.005 P2
UM MAUM10 0.004 P2
UM MAUM11 0.004 P2
UM MAUM12 0.008 P2
UM MAUM13 0.005 P2
UM MAUM14 0.003 P2
UM MAUM15 0.003 P2
UM MAUM16 0.018 P2
UM MAUM17 0.004 P2
UM MAUM18 0.005 P2
UM MAUM19 0.004 P2
UM MAUM20 0.004 P2
MM MAMM1 0.005 P2
MM MAMM2 0.005 P2
MM MAMM3 0.003 P2
MM MAMM4 0.031 P2
MM MAMM5 0.007 P2
MM MAMM6 0.009 P2
MM MAMM7 0.004 P2
MM MAMM8 0.004 P2
MM MAMM9 0.004 P2
MM MAMM10 0.004 P2
MM MAMM11 0.003 P2
MM MAMM12 0.013 P2
MM MAMM13 0.004 P2
MM MAMM14 0.004 P2
MM MAMM15 0.003 P2
MM MAMM16 0.003 P2
MM MAMM17 0.006 P2
MM MAMM18 0.006 P2
MM MAMM19 0.003 P2
MM MAMM20 0.02 P2
LM MALM1 0.003 P2
LM MALM2 0.006 P2
LM MALM3 0.009 P2
LM MALM4 0.004 P2
LM MALM5 0.006 P2
LM MALM6 0.004 P2
LM MALM7 0.004 P2
LM MALM8 0.004 P2
LM MALM9 0.003 P2
LM MALM10 0.005 P2
LM MALM11 0.009 P2
LM MALM12 0.004 P2
LM MALM13 0.008 P2
LM MALM14 0.008 P2
LM MALM15 0.012 P2
LM MALM16 0.004 P2
LM MALM17 0.009 P2
LM MALM18 0.007 P2
LM MALM19 0.024 P2
LM MALM20 0.004 P2
UK MAUK1 0.991 P2
UK MAUK2 0.99 P2
UK MAUK3 0.976 P2
UK MAUK4 0.992 P2
UK MAUK5 0.986 P2
UK MAUK6 0.987 P2
UK MAUK7 0.984 P2
UK MAUK8 0.931 P2
UK MAUK9 0.99 P2
UK MAUK10 0.991 P2
UK MAUK11 0.967 P2
UK MAUK12 0.992 P2
UK MAUK13 0.989 P2
UK MAUK14 0.984 P2
UK MAUK15 0.99 P2
UK MAUK16 0.99 P2
UK MAUK17 0.924 P2
UK MAUK18 0.991 P2
UK MAUK19 0.985 P2
UK MAUK20 0.979 P2
MK MAMK1 0.99 P2
MK MAMK2 0.991 P2
MK MAMK3 0.97 P2
MK MAMK4 0.979 P2
MK MAMK5 0.99 P2
MK MAMK6 0.986 P2
MK MAMK7 0.994 P2
MK MAMK8 0.981 P2
MK MAMK9 0.99 P2
MK MAMK10 0.983 P2
MK MAMK11 0.993 P2
MK MAMK12 0.989 P2
MK MAMK13 0.976 P2
MK MAMK14 0.993 P2
MK MAMK15 0.987 P2
MK MAMK16 0.993 P2
MK MAMK17 0.99 P2
MK MAMK18 0.985 P2
MK MAMK19 0.986 P2
MK MAMK20 0.986 P2
LK MALK1 0.968 P2
LK MALK2 0.943 P2
LK MALK3 0.977 P2
LK MALK4 0.977 P2
LK MALK5 0.812 P2
LK MALK6 0.929 P2
LK MALK7 0.879 P2
LK MALK8 0.992 P2
LK MALK9 0.988 P2
LK MALK10 0.704 P2
LK MALK11 0.992 P2
LK MALK12 0.992 P2
LK MALK13 0.985 P2
LK MALK14 0.983 P2
LK MALK15 0.987 P2
LK MALK16 0.986 P2
LK MALK17 0.985 P2
LK MALK18 0.988 P2
LK MALK19 0.981 P2
LK MALK21 0.989 P2
UD MAUD13 0.005 P3
UD MAUD14 0.005 P3
UD MAUD15 0.006 P3
UD MAUD16 0.008 P3
UD MAUD17 0.007 P3
UD MAUD18 0.048 P3
UD MAUD19 0.041 P3
UD MAUD21 0.006 P3
UD MAUD23 0.016 P3
MD MAMD1 0.011 P3
MD MAMD2 0.024 P3
MD MAMD3 0.004 P3
MD MAMD4 0.023 P3
MD MAMD5 0.026 P3
MD MAMD6 0.004 P3
MD MAMD7 0.011 P3
LD MALD1 0.017 P3
LD MALD2 0.005 P3
LD MALD3 0.009 P3
LD MALD4 0.014 P3
LD MALD5 0.026 P3
LD MALD6 0.014 P3
LD MALD7 0.005 P3
LD MALD8 0.051 P3
LD MALD9 0.013 P3
LD MALD10 0.007 P3
LD MALD12 0.044 P3
LD MALD13 0.005 P3
LD MALD14 0.01 P3
LD MALD15 0.009 P3
LD MALD16 0.005 P3
LD MALD17 0.05 P3
LD MALD18 0.005 P3
LD MALD19 0.007 P3
LD MALD20 0.006 P3
LD MALD21 0.009 P3
LD MALD23 0.003 P3
LD MALD24 0.007 P3
LD MALD25 0.008 P3
LD MALD26 0.012 P3
LD MALD27 0.006 P3
LD MALD28 0.004 P3
LD MALD29 0.004 P3
LD MALD30 0.008 P3
UM MAUM1 0.003 P3
UM MAUM2 0.007 P3
UM MAUM3 0.009 P3
UM MAUM4 0.01 P3
UM MAUM5 0.007 P3
UM MAUM6 0.003 P3
UM MAUM7 0.007 P3
UM MAUM8 0.005 P3
UM MAUM9 0.003 P3
UM MAUM10 0.008 P3
UM MAUM11 0.003 P3
UM MAUM12 0.007 P3
UM MAUM13 0.005 P3
UM MAUM14 0.004 P3
UM MAUM15 0.003 P3
UM MAUM16 0.004 P3
UM MAUM17 0.004 P3
UM MAUM18 0.005 P3
UM MAUM19 0.005 P3
UM MAUM20 0.006 P3
MM MAMM1 0.009 P3
MM MAMM2 0.004 P3
MM MAMM3 0.004 P3
MM MAMM4 0.009 P3
MM MAMM5 0.006 P3
MM MAMM6 0.008 P3
MM MAMM7 0.004 P3
MM MAMM8 0.003 P3
MM MAMM9 0.003 P3
MM MAMM10 0.005 P3
MM MAMM11 0.003 P3
MM MAMM12 0.005 P3
MM MAMM13 0.007 P3
MM MAMM14 0.005 P3
MM MAMM15 0.004 P3
MM MAMM16 0.004 P3
MM MAMM17 0.005 P3
MM MAMM18 0.003 P3
MM MAMM19 0.006 P3
MM MAMM20 0.006 P3
LM MALM1 0.993 P3
LM MALM2 0.991 P3
LM MALM3 0.985 P3
LM MALM4 0.992 P3
LM MALM5 0.99 P3
LM MALM6 0.992 P3
LM MALM7 0.993 P3
LM MALM8 0.993 P3
LM MALM9 0.994 P3
LM MALM10 0.992 P3
LM MALM11 0.987 P3
LM MALM12 0.993 P3
LM MALM13 0.972 P3
LM MALM14 0.989 P3
LM MALM15 0.986 P3
LM MALM16 0.993 P3
LM MALM17 0.986 P3
LM MALM18 0.988 P3
LM MALM19 0.966 P3
LM MALM20 0.992 P3
UK MAUK1 0.006 P3
UK MAUK2 0.005 P3
UK MAUK3 0.02 P3
UK MAUK4 0.005 P3
UK MAUK5 0.01 P3
UK MAUK6 0.009 P3
UK MAUK7 0.012 P3
UK MAUK8 0.025 P3
UK MAUK9 0.004 P3
UK MAUK10 0.006 P3
UK MAUK11 0.026 P3
UK MAUK12 0.004 P3
UK MAUK13 0.007 P3
UK MAUK14 0.012 P3
UK MAUK15 0.007 P3
UK MAUK16 0.005 P3
UK MAUK17 0.059 P3
UK MAUK18 0.005 P3
UK MAUK19 0.008 P3
UK MAUK20 0.014 P3
MK MAMK1 0.004 P3
MK MAMK2 0.004 P3
MK MAMK3 0.007 P3
MK MAMK4 0.012 P3
MK MAMK5 0.003 P3
MK MAMK6 0.006 P3
MK MAMK7 0.003 P3
MK MAMK8 0.004 P3
MK MAMK9 0.005 P3
MK MAMK10 0.006 P3
MK MAMK11 0.004 P3
MK MAMK12 0.007 P3
MK MAMK13 0.005 P3
MK MAMK14 0.004 P3
MK MAMK15 0.005 P3
MK MAMK16 0.003 P3
MK MAMK17 0.006 P3
MK MAMK18 0.003 P3
MK MAMK19 0.008 P3
MK MAMK20 0.008 P3
LK MALK1 0.024 P3
LK MALK2 0.047 P3
LK MALK3 0.02 P3
LK MALK4 0.013 P3
LK MALK5 0.166 P3
LK MALK6 0.008 P3
LK MALK7 0.04 P3
LK MALK8 0.005 P3
LK MALK9 0.007 P3
LK MALK10 0.228 P3
LK MALK11 0.005 P3
LK MALK12 0.004 P3
LK MALK13 0.011 P3
LK MALK14 0.009 P3
LK MALK15 0.007 P3
LK MALK16 0.007 P3
LK MALK17 0.004 P3
LK MALK18 0.007 P3
LK MALK19 0.012 P3
LK MALK21 0.007 P3
使用代码:
pop <- read.csv("2019Nov5_StructurePlotV2_MA1.csv")
ggplot(data=pop, aes(x=Ind, y=pop_est, fill=K)) +
geom_bar(stat="identity") +
xlab("Population") + ylab("Membership Estimate")
我生成了以下图:(https://i.imgur.com/5crF4X3.png)
这看起来像是我所追求的目标的开始,但是我需要x轴标签来反映人口群体(来自“群体”列)而不是每个个体(这显然很混乱)。
我是ggplot2的新手(总体来说R还是很绿色),所以我希望我有所了解。
我到处找了一些其他人,他们可能已经使用ggplot2来操纵STRUCTURE图,因为它是一种广泛使用的群体遗传工具,并且认为可能已经编写了一些管道。令人惊讶的是,情况似乎并非如此,因此,如果有人知道我在这方面可能被忽略的任何事情,请告诉我。
干杯!
答案 0 :(得分:0)
这与我的示例情节差不多。主要技巧是使用刻面作为x轴标签。假设zz
是您提供但引用的数据。
pop <- read.table(text = zz, header = T)
ggplot(data=pop, aes(x=Ind, y=pop_est, fill=K)) +
# Friendly reminder, geom_col is shorthand for geom_bar(stat = "identity")
geom_col(width = 1) +
# Facet over the groups
facet_grid(~ Group, switch = "x", scales = "free", space = "free") +
# Use these expand arguments to get rid of padding around the axes
scale_x_discrete(expand = c(0,0), name = "Population") +
scale_y_continuous(expand = c(0,0), name = "Membership Estimate") +
# We're hiding most of the x-axis and the spacing between panels
theme(panel.spacing.x = grid::unit(0, "cm"),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank(),
panel.border = element_rect(fill = NA, colour = "black"))