ggplot2 中的标准偏差与数据不匹配并且在图中看起来很奇怪
standard deviation in ggplo2 does not match data and looks strange in graph
我正在尝试使用 ggplot2 以图形方式表示我的数据的标准差。我已经来过这里一次，寻求代码另一部分的帮助，一些人非常友好地帮助了我。但是，我 运行 遇到了一些问题。我想放一个较小的数据样本，但我认为在这种情况下，由于我将进一步解释的问题，可能会遗漏一些东西。请原谅巨大的 dput:
> dput(EGG)
structure(list(day = c("0", "0", "0", "0", "0", "0", "7", "7",
"7", "7", "7", "7", "14", "14", "14", "14", "14", "14", "21",
"21", "21", "21", "21", "21", "28", "28", "28", "28", "28", "28",
"0", "0", "0", "0", "0", "0", "7", "7", "7", "7", "7", "7", "14",
"14", "14", "14", "14", "14", "21", "21", "21", "21", "21", "21",
"28", "28", "28", "28", "28", "28", "0", "0", "0", "0", "0",
"0", "7", "7", "7", "7", "7", "7", "14", "14", "14", "14", "14",
"14", "21", "21", "21", "21", "21", "21", "28", "28", "28", "28",
"28", "28", "0", "0", "0", "0", "0", "0", "7", "7", "7", "7",
"7", "7", "14", "14", "14", "14", "14", "14", "21", "21", "21",
"21", "21", "21", "28", "28", "28", "28", "28", "28", "0", "0",
"0", "0", "0", "0", "7", "7", "7", "7", "7", "7", "14", "14",
"14", "14", "14", "14", "21", "21", "21", "21", "21", "21", "28",
"28", "28", "28", "28", "28", "0", "0", "0", "0", "0", "0", "7",
"7", "7", "7", "7", "7", "14", "14", "14", "14", "14", "14",
"21", "21", "21", "21", "21", "21", "28", "28", "28", "28", "28",
"28", "0", "0", "0", "0", "0", "0", "7", "7", "7", "7", "7",
"7", "14", "14", "14", "14", "14", "14", "21", "21", "21", "21",
"21", "21", "28", "28", "28", "28", "28", "28"), chemcon = c(15.5220395247868,
9.06570359183137, 13.8392220116086, 10.0864401981599, 13.940373396987,
14.5688, 14.4688, 13.7392220116086, 13.7504076433121, 10.3938523092218,
17.7940351604959, 13.790373396987, 17.8440351604959, 13.9164076433121,
8.91570359183137, 7.85248618100562, 18.1470351604959, 13.6892220116086,
14.4188, 15.6613170443075, 15.3720395247868, 13.8762220116086,
9.26870359183137, 8.15548618100562, 9.10270359183138, 15.5590395247868,
12.6443936693897, 14.6058, 10.3438523092218, 13.6134076433121,
12.7443936693897, 13.7134076433121, 7.95248618100562, 10.4938523092218,
17.9440351604959, 15.7613170443075, 15.9166319769788, 16.0236161993658,
14.449820053383, 23.6434916258293, 29.23, 16.6136319769788, 14.4337543105197,
25.8571621909037, 27.2488509180735, 26.3405437141942, 26.6088509180735,
12.3358365758755, 10.5308523092218, 15.7506319769788, 25.6435437141942,
26.9373074696005, 21.880025633791, 15.9606007018431, 12.5943936693897,
15.7983170443075, 25.2859002423082, 31.4473460721868, 22.683460279146,
25.9829002423082, 11.82042, 15.5199002423082, 16.6636161993658,
15.089820053383, 13.03551, 9.48875, 25.7405437141942, 18.6937124658781,
30.7973460721868, 22.033460279146, 18.7437124658781, 25.6905437141942,
25.7915437141942, 30.8473460721868, 22.083460279146, 18.8807124658781,
25.3329002423082, 15.9636319769788, 25.6859002423082, 16.3166319769788,
26.0435437141942, 22.220460279146, 25.5199002423082, 16.1506319769788,
25.8775437141942, 19.0467124658781, 31.1503460721868, 22.386460279146,
25.3829002423082, 16.0136319769788, 14.143373396987, 8.96570359183137,
12.7813936693897, 13.5634076433121, 13.977373396987, 15.9643170443075,
25.5199002423082, 30.5559941059036, 32.419, 34.0709071343396,
36.9364807907246, 49.7582480724103, 39.5201, 55.8759773695839,
45.219463429644, 41.3352176220807, 35.1199, 51.813050421884,
41.6932176220807, 38.8525423728814, 40.1979941059036, 56.6606438665008,
51.6796783998212, 44.861463429644, 36.6956947393253, 51.455050421884,
56.2339773695839, 53.3216783998212, 64.124863506094, 37.0536947393253,
5.293902130258, 17.55457, 9.98644019815995, 15.7250395247868,
15.6113170443075, 13.840373396987, 20.9572380860577, 23.361216730038,
25.6685910032803, 16.1506319769788, 25.6859002423082, 16.3166319769788,
26.5473074696005, 21.490025633791, 15.5706007018431, 14.0437543105197,
25.4671621909037, 17.9810351604959, 23.1734916258293, 38.7599759195535,
16.1936161993658, 14.619820053383, 26.7788509180735, 12.5058365758755,
18.8437124658781, 30.9473460721868, 22.183460279146, 25.4829002423082,
16.1136319769788, 25.8405437141942, 18.7764641729212, 15.4965541256184,
14.0422220116086, 7.98948618100562, 15.4220395247868, 10.1234401981599,
18.7947124658781, 23.3114, 26.99513, 18.7447124658781, 30.8483460721868,
22.084460279146, 24.0930028246135, 31.7642972700841, 20.0491670749633,
27.7456849010516, 26.026400413152, 25.2619728008263, 26.0435437141942,
22.220460279146, 25.1700273310577, 27.6462189543881, 24.8183371992736,
32.1328682890728, 23.6425352458789, 28.3907888290054, 36.0970516777201,
24.7983371992736, 25.7415437141942, 30.9843460721868, 9.93644019815994,
7.80248618100562, 10.6968523092218, 10.2894401981599, 14.7718,
12.9473936693897, 36.0500998193745, 27.962318404467, 50.8635290067137,
33.3141610679696, 31.6036504707596, 44.4839329775636, 41.6817324840764,
45.3996004974937, 44.5523364548183, 45.6550955414013, 50.2946957467359,
41.0826507304484, 54.066863506094, 45.161463429644, 49.7002480724103,
39.1525423728814, 45.4979941059036, 41.6352176220807, 51.6216783998212,
46.9956947393253, 51.755050421884, 50.6026438665008, 53.1759773695839,
52.3618577776276), type = c("control", "control", "control",
"control", "control", "control", "control", "control", "control",
"control", "control", "control", "control", "control", "control",
"control", "control", "control", "control", "control", "control",
"control", "control", "control", "control", "control", "control",
"control", "control", "control", "nZn1", "nZn1", "nZn1", "nZn1",
"nZn1", "nZn1", "nZn1", "nZn1", "nZn1", "nZn1", "nZn1", "nZn1",
"nZn1", "nZn1", "nZn1", "nZn1", "nZn1", "nZn1", "nZn1", "nZn1",
"nZn1", "nZn1", "nZn1", "nZn1", "nZn1", "nZn1", "nZn1", "nZn1",
"nZn1", "nZn1", "nZn10", "nZn10", "nZn10", "nZn10", "nZn10",
"nZn10", "nZn10", "nZn10", "nZn10", "nZn10", "nZn10", "nZn10",
"nZn10", "nZn10", "nZn10", "nZn10", "nZn10", "nZn10", "nZn10",
"nZn10", "nZn10", "nZn10", "nZn10", "nZn10", "nZn10", "nZn10",
"nZn10", "nZn10", "nZn10", "nZn10", "nZn100", "nZn100", "nZn100",
"nZn100", "nZn100", "nZn100", "nZn100", "nZn100", "nZn100", "nZn100",
"nZn100", "nZn100", "nZn100", "nZn100", "nZn100", "nZn100", "nZn100",
"nZn100", "nZn100", "nZn100", "nZn100", "nZn100", "nZn100", "nZn100",
"nZn100", "nZn100", "nZn100", "nZn100", "nZn100", "nZn100", "Zn1",
"Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1",
"Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1",
"Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1",
"Zn1", "Zn1", "Zn10", "Zn10", "Zn10", "Zn10", "Zn10", "Zn10",
"Zn10", "Zn10", "Zn10", "Zn10", "Zn10", "Zn10", "Zn10", "Zn10",
"Zn10", "Zn10", "Zn10", "Zn10", "Zn10", "Zn10", "Zn10", "Zn10",
"Zn10", "Zn10", "Zn10", "Zn10", "Zn10", "Zn10", "Zn10", "Zn10",
"Zn100", "Zn100", "Zn100", "Zn100", "Zn100", "Zn100", "Zn100",
"Zn100", "Zn100", "Zn100", "Zn100", "Zn100", "Zn100", "Zn100",
"Zn100", "Zn100", "Zn100", "Zn100", "Zn100", "Zn100", "Zn100",
"Zn100", "Zn100", "Zn100", "Zn100", "Zn100", "Zn100", "Zn100",
"Zn100", "Zn100")), row.names = c(NA, -210L), class = c("tbl_df",
"tbl", "data.frame"))
head(EGG)
# A tibble: 6 x 3
day chemcon type
<chr> <dbl> <chr>
1 0 15.5 control
2 0 9.07 control
3 0 13.8 control
4 0 10.1 control
5 0 13.9 control
6 0 14.6 control
到目前为止，这是我的代码：
library(ggplot2)
Figure1 <- ggplot(EGG,aes(x = type, y = chemcon, fill = day))
Figure1 +
geom_bar(stat="identity", position= "dodge") + #nb you can just use 'dodge' in barplots
scale_fill_brewer(palette="Paired")+
theme_minimal() +
labs(x="", y="chemcon") +
theme(panel.background = element_blank(),
axis.line = element_line(colour = "black"),
panel.grid=element_blank()) +
geom_errorbar(aes(ymin = chemcon - .5 * sd(chemcon),
ymax = chemcon + .5 * sd(chemcon)),
position = "dodge")
这是我感谢本网站某人的初始代码。不幸的是，它在 StDev 方面似乎效果不佳。
然后我尝试用以下内容替换 geom_errorbar 位：
stat_summary(fun.data=mean_cl_boot,
geom="errorbar",
width=0.2,
position=position_dodge(width=0.90))
#####
stat_summary(fun.data=mean_sdl,
geom="errorbar",
width=0.2,
position=position_dodge(width=0.90))
########
stat_summary(fun.data = mean_se, geom = 'errorbar', position = 'dodge')
结果如下：2 3 4
如你所见，没有什么是我想要的。我特别想要图中每个 bar/section 的标准偏差（例如，对于第 7 天和类型 Zn100，chemcon 的 StDev 是多少？）。这些太多或不合适。
（我提供的 excel 图片有问题，因为最初制作它的人只是告诉我忽略它）
首先计算一个数据集（在代码中称为 cc），每个 group/pair 只有均值和 SD。在你的例子中，5*7=35 对。然后用这个来绘制你的数据。我个人尝试自己计算要显示的数据，而不是让函数来计算。恕我直言，它不太容易出错。
aa <- aggregate(chemcon ~ day + type, data=EGG, FUN=mean)
bb <- aggregate(chemcon ~ day + type, data=EGG, FUN=sd)
cc <- merge(aa, bb, by=c("day", "type"))
colnames(cc)[3:4] <- c("mean", "sd")
ggplot(cc, aes(x = type, y = mean, fill = day))+
geom_bar(stat="identity", position= "dodge") + #nb you can just use 'dodge' in barplots
scale_fill_brewer(palette="Paired")+
theme_minimal() +
labs(x="", y="chemcon") +
theme(panel.background = element_blank(),
axis.line = element_line(colour = "black"),
panel.grid=element_blank()) +
geom_errorbar(aes(ymin = mean-sd,
ymax = mean+sd),
position = "dodge")
我正在尝试使用 ggplot2 以图形方式表示我的数据的标准差。我已经来过这里一次，寻求代码另一部分的帮助，一些人非常友好地帮助了我。但是，我 运行 遇到了一些问题。我想放一个较小的数据样本，但我认为在这种情况下，由于我将进一步解释的问题，可能会遗漏一些东西。请原谅巨大的 dput:
> dput(EGG)
structure(list(day = c("0", "0", "0", "0", "0", "0", "7", "7",
"7", "7", "7", "7", "14", "14", "14", "14", "14", "14", "21",
"21", "21", "21", "21", "21", "28", "28", "28", "28", "28", "28",
"0", "0", "0", "0", "0", "0", "7", "7", "7", "7", "7", "7", "14",
"14", "14", "14", "14", "14", "21", "21", "21", "21", "21", "21",
"28", "28", "28", "28", "28", "28", "0", "0", "0", "0", "0",
"0", "7", "7", "7", "7", "7", "7", "14", "14", "14", "14", "14",
"14", "21", "21", "21", "21", "21", "21", "28", "28", "28", "28",
"28", "28", "0", "0", "0", "0", "0", "0", "7", "7", "7", "7",
"7", "7", "14", "14", "14", "14", "14", "14", "21", "21", "21",
"21", "21", "21", "28", "28", "28", "28", "28", "28", "0", "0",
"0", "0", "0", "0", "7", "7", "7", "7", "7", "7", "14", "14",
"14", "14", "14", "14", "21", "21", "21", "21", "21", "21", "28",
"28", "28", "28", "28", "28", "0", "0", "0", "0", "0", "0", "7",
"7", "7", "7", "7", "7", "14", "14", "14", "14", "14", "14",
"21", "21", "21", "21", "21", "21", "28", "28", "28", "28", "28",
"28", "0", "0", "0", "0", "0", "0", "7", "7", "7", "7", "7",
"7", "14", "14", "14", "14", "14", "14", "21", "21", "21", "21",
"21", "21", "28", "28", "28", "28", "28", "28"), chemcon = c(15.5220395247868,
9.06570359183137, 13.8392220116086, 10.0864401981599, 13.940373396987,
14.5688, 14.4688, 13.7392220116086, 13.7504076433121, 10.3938523092218,
17.7940351604959, 13.790373396987, 17.8440351604959, 13.9164076433121,
8.91570359183137, 7.85248618100562, 18.1470351604959, 13.6892220116086,
14.4188, 15.6613170443075, 15.3720395247868, 13.8762220116086,
9.26870359183137, 8.15548618100562, 9.10270359183138, 15.5590395247868,
12.6443936693897, 14.6058, 10.3438523092218, 13.6134076433121,
12.7443936693897, 13.7134076433121, 7.95248618100562, 10.4938523092218,
17.9440351604959, 15.7613170443075, 15.9166319769788, 16.0236161993658,
14.449820053383, 23.6434916258293, 29.23, 16.6136319769788, 14.4337543105197,
25.8571621909037, 27.2488509180735, 26.3405437141942, 26.6088509180735,
12.3358365758755, 10.5308523092218, 15.7506319769788, 25.6435437141942,
26.9373074696005, 21.880025633791, 15.9606007018431, 12.5943936693897,
15.7983170443075, 25.2859002423082, 31.4473460721868, 22.683460279146,
25.9829002423082, 11.82042, 15.5199002423082, 16.6636161993658,
15.089820053383, 13.03551, 9.48875, 25.7405437141942, 18.6937124658781,
30.7973460721868, 22.033460279146, 18.7437124658781, 25.6905437141942,
25.7915437141942, 30.8473460721868, 22.083460279146, 18.8807124658781,
25.3329002423082, 15.9636319769788, 25.6859002423082, 16.3166319769788,
26.0435437141942, 22.220460279146, 25.5199002423082, 16.1506319769788,
25.8775437141942, 19.0467124658781, 31.1503460721868, 22.386460279146,
25.3829002423082, 16.0136319769788, 14.143373396987, 8.96570359183137,
12.7813936693897, 13.5634076433121, 13.977373396987, 15.9643170443075,
25.5199002423082, 30.5559941059036, 32.419, 34.0709071343396,
36.9364807907246, 49.7582480724103, 39.5201, 55.8759773695839,
45.219463429644, 41.3352176220807, 35.1199, 51.813050421884,
41.6932176220807, 38.8525423728814, 40.1979941059036, 56.6606438665008,
51.6796783998212, 44.861463429644, 36.6956947393253, 51.455050421884,
56.2339773695839, 53.3216783998212, 64.124863506094, 37.0536947393253,
5.293902130258, 17.55457, 9.98644019815995, 15.7250395247868,
15.6113170443075, 13.840373396987, 20.9572380860577, 23.361216730038,
25.6685910032803, 16.1506319769788, 25.6859002423082, 16.3166319769788,
26.5473074696005, 21.490025633791, 15.5706007018431, 14.0437543105197,
25.4671621909037, 17.9810351604959, 23.1734916258293, 38.7599759195535,
16.1936161993658, 14.619820053383, 26.7788509180735, 12.5058365758755,
18.8437124658781, 30.9473460721868, 22.183460279146, 25.4829002423082,
16.1136319769788, 25.8405437141942, 18.7764641729212, 15.4965541256184,
14.0422220116086, 7.98948618100562, 15.4220395247868, 10.1234401981599,
18.7947124658781, 23.3114, 26.99513, 18.7447124658781, 30.8483460721868,
22.084460279146, 24.0930028246135, 31.7642972700841, 20.0491670749633,
27.7456849010516, 26.026400413152, 25.2619728008263, 26.0435437141942,
22.220460279146, 25.1700273310577, 27.6462189543881, 24.8183371992736,
32.1328682890728, 23.6425352458789, 28.3907888290054, 36.0970516777201,
24.7983371992736, 25.7415437141942, 30.9843460721868, 9.93644019815994,
7.80248618100562, 10.6968523092218, 10.2894401981599, 14.7718,
12.9473936693897, 36.0500998193745, 27.962318404467, 50.8635290067137,
33.3141610679696, 31.6036504707596, 44.4839329775636, 41.6817324840764,
45.3996004974937, 44.5523364548183, 45.6550955414013, 50.2946957467359,
41.0826507304484, 54.066863506094, 45.161463429644, 49.7002480724103,
39.1525423728814, 45.4979941059036, 41.6352176220807, 51.6216783998212,
46.9956947393253, 51.755050421884, 50.6026438665008, 53.1759773695839,
52.3618577776276), type = c("control", "control", "control",
"control", "control", "control", "control", "control", "control",
"control", "control", "control", "control", "control", "control",
"control", "control", "control", "control", "control", "control",
"control", "control", "control", "control", "control", "control",
"control", "control", "control", "nZn1", "nZn1", "nZn1", "nZn1",
"nZn1", "nZn1", "nZn1", "nZn1", "nZn1", "nZn1", "nZn1", "nZn1",
"nZn1", "nZn1", "nZn1", "nZn1", "nZn1", "nZn1", "nZn1", "nZn1",
"nZn1", "nZn1", "nZn1", "nZn1", "nZn1", "nZn1", "nZn1", "nZn1",
"nZn1", "nZn1", "nZn10", "nZn10", "nZn10", "nZn10", "nZn10",
"nZn10", "nZn10", "nZn10", "nZn10", "nZn10", "nZn10", "nZn10",
"nZn10", "nZn10", "nZn10", "nZn10", "nZn10", "nZn10", "nZn10",
"nZn10", "nZn10", "nZn10", "nZn10", "nZn10", "nZn10", "nZn10",
"nZn10", "nZn10", "nZn10", "nZn10", "nZn100", "nZn100", "nZn100",
"nZn100", "nZn100", "nZn100", "nZn100", "nZn100", "nZn100", "nZn100",
"nZn100", "nZn100", "nZn100", "nZn100", "nZn100", "nZn100", "nZn100",
"nZn100", "nZn100", "nZn100", "nZn100", "nZn100", "nZn100", "nZn100",
"nZn100", "nZn100", "nZn100", "nZn100", "nZn100", "nZn100", "Zn1",
"Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1",
"Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1",
"Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1", "Zn1",
"Zn1", "Zn1", "Zn10", "Zn10", "Zn10", "Zn10", "Zn10", "Zn10",
"Zn10", "Zn10", "Zn10", "Zn10", "Zn10", "Zn10", "Zn10", "Zn10",
"Zn10", "Zn10", "Zn10", "Zn10", "Zn10", "Zn10", "Zn10", "Zn10",
"Zn10", "Zn10", "Zn10", "Zn10", "Zn10", "Zn10", "Zn10", "Zn10",
"Zn100", "Zn100", "Zn100", "Zn100", "Zn100", "Zn100", "Zn100",
"Zn100", "Zn100", "Zn100", "Zn100", "Zn100", "Zn100", "Zn100",
"Zn100", "Zn100", "Zn100", "Zn100", "Zn100", "Zn100", "Zn100",
"Zn100", "Zn100", "Zn100", "Zn100", "Zn100", "Zn100", "Zn100",
"Zn100", "Zn100")), row.names = c(NA, -210L), class = c("tbl_df",
"tbl", "data.frame"))
head(EGG)
# A tibble: 6 x 3
day chemcon type
<chr> <dbl> <chr>
1 0 15.5 control
2 0 9.07 control
3 0 13.8 control
4 0 10.1 control
5 0 13.9 control
6 0 14.6 control
到目前为止，这是我的代码：
library(ggplot2)
Figure1 <- ggplot(EGG,aes(x = type, y = chemcon, fill = day))
Figure1 +
geom_bar(stat="identity", position= "dodge") + #nb you can just use 'dodge' in barplots
scale_fill_brewer(palette="Paired")+
theme_minimal() +
labs(x="", y="chemcon") +
theme(panel.background = element_blank(),
axis.line = element_line(colour = "black"),
panel.grid=element_blank()) +
geom_errorbar(aes(ymin = chemcon - .5 * sd(chemcon),
ymax = chemcon + .5 * sd(chemcon)),
position = "dodge")
这是我感谢本网站某人的初始代码。不幸的是，它在 StDev 方面似乎效果不佳。
然后我尝试用以下内容替换 geom_errorbar 位：
stat_summary(fun.data=mean_cl_boot,
geom="errorbar",
width=0.2,
position=position_dodge(width=0.90))
#####
stat_summary(fun.data=mean_sdl,
geom="errorbar",
width=0.2,
position=position_dodge(width=0.90))
########
stat_summary(fun.data = mean_se, geom = 'errorbar', position = 'dodge')
结果如下：2 3 4
如你所见，没有什么是我想要的。我特别想要图中每个 bar/section 的标准偏差（例如，对于第 7 天和类型 Zn100，chemcon 的 StDev 是多少？）。这些太多或不合适。
（我提供的 excel 图片有问题，因为最初制作它的人只是告诉我忽略它）
首先计算一个数据集（在代码中称为 cc），每个 group/pair 只有均值和 SD。在你的例子中，5*7=35 对。然后用这个来绘制你的数据。我个人尝试自己计算要显示的数据，而不是让函数来计算。恕我直言，它不太容易出错。
aa <- aggregate(chemcon ~ day + type, data=EGG, FUN=mean)
bb <- aggregate(chemcon ~ day + type, data=EGG, FUN=sd)
cc <- merge(aa, bb, by=c("day", "type"))
colnames(cc)[3:4] <- c("mean", "sd")
ggplot(cc, aes(x = type, y = mean, fill = day))+
geom_bar(stat="identity", position= "dodge") + #nb you can just use 'dodge' in barplots
scale_fill_brewer(palette="Paired")+
theme_minimal() +
labs(x="", y="chemcon") +
theme(panel.background = element_blank(),
axis.line = element_line(colour = "black"),
panel.grid=element_blank()) +
geom_errorbar(aes(ymin = mean-sd,
ymax = mean+sd),
position = "dodge")