我正在尝试使用ggplot绘制具有多组美学效果的多面板和多线图facet_wrap
。但是,geom_smooth
当一组数据点太少时,构面图中的所有线都将失败。
plot1 <- ggplot(data=df1,
aes(x=Year, y=Mean, group=Group2, linetype=Group2, shape=Group2)) +
geom_errorbar(aes(ymin=Mean-SE, ymax=Mean+SE), width=0.2) +
geom_smooth(method = "gam", se=F, formula = y ~ s(x, k=3), size = 1, colour="black") +
geom_point(position=pd, size=2, fill="white") +
scale_x_continuous(limits=c(min(df1$Year-0.1), max(df1$Year+0.1)),
breaks=seq(min(df1$Year),max(df1$Year),5)) +
facet_wrap(~Group1, scales = "free", ncol=2) +
theme_bw() +
theme(axis.text.x = element_text(),
axis.title.x = element_blank(),
strip.background = element_blank(),
axis.line.x = element_line(colour="black"),
axis.line.y = element_line(colour="black"),
panel.grid.minor = element_blank(),
panel.grid.major = element_blank(),
panel.border = element_blank(),
panel.background = element_blank(),
legend.position="top",
legend.title = element_blank())
plot(plot1)
产生以下图。这仅是摘要数据,以使其更容易。就像错误使ggplot停止计算该特定平面上的序列平滑一样。
数据
Year Group1 Group2 Mean SE
2011 Factor A Factor C 30.62089116 3.672624771
2011 Factor A Factor D 54.99066324 2.822405771
2011 Factor B Factor C 30.48859003 3.748388489
2011 Factor B Factor D 45.70410611 4.284244405
2017 Factor A Factor C 33.68256601 4.030964172
2017 Factor A Factor D 53.43496462 4.687042033
2017 Factor B Factor C 23.08799875 5.17753488
2001 Factor A Factor C 23.79166667 2.837795432
2001 Factor A Factor D 23.75925926 3.688185081
2001 Factor B Factor C 29.05555556 4.08597798
2001 Factor B Factor D 28.13333333 7.877429079
2008 Factor A Factor C 23.3 2.383624691
2008 Factor A Factor D 28.83333333 2.750959429
2008 Factor B Factor C 34.01666667 5.340999698
和情节
显然,有足够的数据为组factorB中的factorC线画一条平滑线。任何的想法?
我认为这很棘手。通过一些测试和阅读后电流GH代码的StatSmooth
,我总结我的调查结果如下:
geom_smooth()
如果任何数据组对AND的观察值太少,则无法在绘图面板中绘制所有平滑线;method = "gam"
formula = y ~ s(x, k = 3)
formula = y ~ x
(即默认公式);"lm"
,"glm"
)使用默认的公式,但也有发生method = "loess"
;我们可以用一些简化的代码重现上面的内容:
# create sample data
n <- 30
set.seed(567)
df.1 <- data.frame( # there is only 1 observation for group == B
x = rnorm(n), y = rnorm(n),
group = c(rep("A", n - 1), rep("B", 1)),
facet = sample(c("X", "Y"), size = n, replace = TRUE))
set.seed(567)
df.2 <- data.frame( # there are 2 observations for group == B
x = rnorm(n), y = rnorm(n),
group = c(rep("A", n - 2), rep("B", 2)),
facet = sample(c("X", "Y"), size = n, replace = TRUE))
# create base plot
p <- ggplot(df.2, aes(x = x, y = y, color = group)) +
geom_point() + theme_bw()
# problem: no smoothed line at all in the entire plot
p + geom_smooth(method = "gam", formula = y ~ s(x, k = 3))
# problem: no smoothed line in the affected panel
p + facet_wrap(~ facet) +
geom_smooth(method = "gam", formula = y ~ s(x, k = 3))
# no problem with default formula: smoothed lines in both facet panels
p + facet_wrap(~ facet) + geom_smooth(method = "gam")
# no problem with lm / glm, but problem with loess
p + facet_wrap(~ facet) + geom_smooth(method = "lm")
p + facet_wrap(~ facet) + geom_smooth(method = "glm")
p + facet_wrap(~ facet) + geom_smooth(method = "loess")
# no problem if there's only one observation (instead of two)
p %+% df.1 + geom_smooth(method = "gam", formula = y ~ s(x, k = 3))
p %+% df.1 + facet_wrap(~ facet) +
geom_smooth(method = "gam", formula = y ~ s(x, k = 3))
意见1和2的解释:
我认为问题的关键在于中的最后两行StatSmooth
的compute_group
功能。第一行调用模型的功能(例如stats::glm
,stats::loess
,mgcv::gam
),用于通过指定的每一组数据帧上aes(group = ...)
的映射,而第二行调用包装器之一的周围stats::predict()
,以获得平滑的值(以及置信区间,如果适用的话),用于模型。
model <- do.call(method, c(base.args, method.args))
predictdf(model, xseq, se, level)
当参数method = "gam", formula = y ~ s(x, k = 3)
仅用于带有两个观察值的数据帧时,将发生以下情况:
model <- do.call(mgcv::gam,
args = list(formula = y ~ s(x, k = 3),
data = df.2 %>% filter(group == "B" & facet == "X")))
smooth.construct.tp.smooth.spec(object,dk $ data,dk $ knots)中的错误:一个术语的唯一协变量组合少于指定的最大自由度
model
,定义为采用的结果的对象do.call(...)
,甚至尚未创建。代码的最后一行predictdf(...)
将抛出错误,因为model
不存在。无刻面,这会影响所有所做的计算StatSmooth
,并且geom_smooth()
没有接收到可用的数据来创建在其层中的任何的geom。使用构面时,将针对每个构面分别进行上述计算,因此仅影响有问题数据的构面会受到影响。
意见3和4的解释:
加上上面的内容,如果我们没有指定公式来替换默认值y ~ x
,我们将从gam
/ lm
/获得一个有效的模型对象glm
,可以将其传递给ggplot2的未导出predictdf
函数以获取预测值的数据帧:
model <- do.call(mgcv::gam, # or stats::lm, stats::glm
args = list(formula = y ~ x,
data = df.2 %>% filter(group == "B" & facet == "X")))
result <- ggplot2:::predictdf(
model,
xseq = seq(-2, 1.5, length.out = 80), # pseudo range of x-axis values
se = FALSE, level = 0.95) # default SE / level parameters
loess
也将返回一个有效的对象,尽管带有大量警告。但是,将其传递给predictdf
将导致错误:
model <- do.call(stats::loess,
args = list(formula = y ~ x,
data = df.2 %>% filter(group == "B" & facet == "X")))
result <- ggplot2:::predictdf(
model,
xseq = seq(-2, 1.5, length.out = 80), # pseudo range of x-axis values
se = FALSE, level = 0.95) # default SE / level parameters
predLoess(object $ y,object $ x,newx = if(is.null(newdata))object $ x else if(is.data.frame(newdata))as.matrix(model.frame(delete.response( terms(object)),:外部函数调用中的NA / NaN / Inf(arg 5)
观察说明5:
StatSmooth
的compute_group
功能从以下内容开始:
if (length(unique(data$x)) < 2) {
# Not enough data to perform fit
return(data.frame())
}
换句话说,如果指定组中只有1个观察值,则StatSmooth
立即返回空白数据帧。因此,它将永远不会到达代码的后续部分以引发任何错误。
查明发生问题的地方后,我们可以对compute_group
代码进行调整(请参阅带注释和注释掉的部分):
new.compute_group <- function(
data, scales, method = "auto", formula = y~x, se = TRUE, n = 80, span = 0.75,
fullrange = FALSE, xseq = NULL, level = 0.95, method.args = list(), na.rm = FALSE) {
if (length(unique(data$x)) < 2) return(data.frame())
if (is.null(data$weight)) data$weight <- 1
if (is.null(xseq)) {
if (is.integer(data$x)) {
if (fullrange) {
xseq <- scales$x$dimension()
} else {
xseq <- sort(unique(data$x))
}
} else {
if (fullrange) {
range <- scales$x$dimension()
} else {
range <- range(data$x, na.rm = TRUE)
}
xseq <- seq(range[1], range[2], length.out = n)
}
}
if (identical(method, "loess")) method.args$span <- span
if (is.character(method)) method <- match.fun(method)
base.args <- list(quote(formula), data = quote(data), weights = quote(weight))
# if modelling fails, return empty data frame
# model <- do.call(method, c(base.args, method.args))
model <- try(do.call(method, c(base.args, method.args)))
if(inherits(model, "try-error")) return(data.frame())
# if modelling didn't fail, but prediction returns NA,
# also return empty data frame
# predictdf(model, xseq, se, level)
pred <- try(ggplot2:::predictdf(model, xseq, se, level))
if(inherits(pred, "try-error")) return(data.frame())
return(pred)
}
定义一个使用此版本的新统计图层:
# same as stat_smooth() except that it uses stat = StatSmooth2, rather
# than StatSmooth
stat_smooth_local <- function(
mapping = NULL, data = NULL, geom = "smooth", position = "identity", ...,
method = "auto", formula = y ~ x, se = TRUE, n = 80, span = 0.75,
fullrange = FALSE, level = 0.95, method.args = list(), na.rm = FALSE,
show.legend = NA, inherit.aes = TRUE) {
layer(
data = data, mapping = mapping, stat = StatSmooth2,
geom = geom, position = position, show.legend = show.legend,
inherit.aes = inherit.aes,
params = list(
method = method, formula = formula, se = se, n = n,
fullrange = fullrange, level = level, na.rm = na.rm,
method.args = method.args, span = span, ...
)
)
}
# inherit from StatSmooth
StatSmooth2 <- ggproto(
"StatSmooth2", ggplot2::StatSmooth,
compute_group = new.compute_group
)
我们可以像以前一样处理相同的情况,替换geom_smooth()
为stat_smooth_local()
,并验证在每种情况下都可以看到平滑的geom图层(请注意,有些图层仍会产生错误消息):
# problem resolved: smoothed line for applicable group in the entire plot
p + stat_smooth_local(method = "gam", formula = y ~ s(x, k = 3))
# problem resolved: smoothed line for applicable group in the affected panel
p + facet_wrap(~ facet) +
stat_smooth_local(method = "gam", formula = y ~ s(x, k = 3))
# still no problem with default formula
p + facet_wrap(~ facet) + stat_smooth_local(method = "gam")
# still no problem with lm / glm; problem resolved for loess
p + facet_wrap(~ facet) + stat_smooth_local(method = "lm")
p + facet_wrap(~ facet) + stat_smooth_local(method = "glm")
p + facet_grid(~ facet) + stat_smooth_local(method = "loess")
# still no problem if there's only one observation (instead of two)
p %+% df.1 + stat_smooth_local(method = "gam", formula = y ~ s(x, k = 3))
p %+% df.1 + facet_wrap(~ facet) +
stat_smooth_local(method = "gam", formula = y ~ s(x, k = 3))
# showing one pair of contrasts here
cowplot::plot_grid(
p + facet_wrap(~ facet) + ggtitle("Before") +
geom_smooth(method = "gam", formula = y ~ s(x, k = 3)),
p + facet_wrap(~ facet) + ggtitle("After") +
stat_smooth_local(method = "gam", formula = y ~ s(x, k = 3)),
nrow = 2
)
本文收集自互联网,转载请注明来源。
如有侵权,请联系 [email protected] 删除。
我来说两句