R Corrplot软件包简介,绘制相关热图

最新推荐文章于 2023-11-18 10:36:22 发布

gavin_cdc

最新推荐文章于 2023-11-18 10:36:22 发布

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分类专栏：作图结果解释 R语言

原文链接： https://cran.r-project.org/web/packages/corrplot/vignettes/corrplot-intro.html

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Corrplot软件包简介

介绍

所述corrplot包是相关矩阵，置信区间的图形显示。它还包含一些进行矩阵重新排序的算法。另外，corrplot擅长细节，包括选择颜色，文本标签，颜色标签，布局等。

可视化方法

有七个可视化方法（参数method中）corrplot包，命名"circle"，"square"，"ellipse"，"number"，"shade"，"color"，"pie"。

正相关以蓝色显示，负相关以红色显示。颜色强度和圆圈的大小与相关系数成正比。

library(corrplot)

## corrplot 0.84 loaded

M <- cor(mtcars)
corrplot(M, method = "circle")

corrplot(M, method = "square")

corrplot(M, method = "ellipse")

corrplot(M, method = "number") # Display the correlation coefficient

corrplot(M, method = "shade")

corrplot(M, method = "color")

corrplot(M, method = "pie")

布局

共有三种布局类型（参数type）：

"full"（默认）：显示完整的相关矩阵
"upper"：显示相关矩阵的上三角
"lower"：显示相关矩阵的下三角

corrplot(M, type = "upper")
corrplot(M, type = "upper")

corrplot.mixed() 是混合可视化样式的包装函数。

corrplot.mixed(M)

corrplot.mixed(M, lower.col = "black", number.cex = .7)

corrplot.mixed(M, lower = "ellipse", upper = "circle")

corrplot.mixed(M, lower = "square", upper = "circle", tl.col = "black")

重新排序相关矩阵

相关矩阵可以根据相关系数重新排序。这对于确定矩阵中隐藏的结构和图案很重要。有在corrplot（参数四种方法order）的名字命名 "AOE"，"FPC"，"hclust"，"alphabet"。在序列化包中可以找到更多算法。

您还可以通过function手动“重新排序”矩阵corrMatOrder()。

"AOE"一个我ai

a i = { 棕褐色（e i 2 / e i 1），如果 ë 我1 > 0 ;棕褐色（e i 2 / e i 1）+ π ，除此以外。ai={tan⁡(ei2/ei1),if ei1>0;tan⁡(ei2/ei1)+π,otherwise.

Ë 1e1Ë 2e2
"FPC" 对于第一个主成分订单。
"hclust"层次聚类顺序，以及"hclust.method"要使用的聚集方法。"hclust.method"应该是一个 "ward"，"single"，"complete"，"average"，"mcquitty"，"median"或 "centroid"。
"alphabet" 按字母顺序排列。

corrplot(M, order = "AOE")

corrplot(M, order = "hclust")

corrplot(M, order = "FPC")

corrplot(M, order = "alphabet")

如果使用"hclust"，则corrplot()可以基于层次聚类的结果在相关矩阵图的周围绘制矩形。

corrplot(M, order = "hclust", addrect = 2)

corrplot(M, order = "hclust", addrect = 3)

# Change background color to lightblue
corrplot(M, type = "upper", order = "hclust",
         col = c("black", "white"), bg = "lightblue")

使用不同的色谱

如上节所示，可以自定义相关图的颜色。该功能colorRampPalette()非常便于生成色谱。

col1 <- colorRampPalette(c("#7F0000", "red", "#FF7F00", "yellow", "white",
                           "cyan", "#007FFF", "blue", "#00007F"))
col2 <- colorRampPalette(c("#67001F", "#B2182B", "#D6604D", "#F4A582",
                           "#FDDBC7", "#FFFFFF", "#D1E5F0", "#92C5DE",
                           "#4393C3", "#2166AC", "#053061"))
col3 <- colorRampPalette(c("red", "white", "blue")) 
col4 <- colorRampPalette(c("#7F0000", "red", "#FF7F00", "yellow", "#7FFF7F",
                           "cyan", "#007FFF", "blue", "#00007F"))
whiteblack <- c("white", "black")

## using these color spectra
corrplot(M, order = "hclust", addrect = 2, col = col1(100))

corrplot(M, order = "hclust", addrect = 2, col = col2(50))

corrplot(M, order = "hclust", addrect = 2, col = col3(20))

corrplot(M, order = "hclust", addrect = 2, col = col4(10))

corrplot(M, order = "hclust", addrect = 2, col = whiteblack, bg = "gold2")

您还可以使用标准调色板（包grDevices）

corrplot(M, order = "hclust", addrect = 2, col = heat.colors(100))

corrplot(M, order = "hclust", addrect = 2, col = terrain.colors(100))

corrplot(M, order = "hclust", addrect = 2, col = cm.colors(100))

corrplot(M, order = "hclust", addrect = 2, col = gray.colors(100))

其他选择是使用RcolorBrewer包。

library(RColorBrewer)

corrplot(M, type = "upper", order = "hclust",
         col = brewer.pal(n = 8, name = "RdBu"))

corrplot(M, type = "upper", order = "hclust",
         col = brewer.pal(n = 8, name = "RdYlBu"))

corrplot(M, type = "upper", order = "hclust",
         col = brewer.pal(n = 8, name = "PuOr"))

更改文本标签和图例的颜色和旋转

参数cl.*用于颜色图例，tl.*如果用于文本图例。对于文本标签，tl.col（文本标签颜色）和tl.srt（文本标签字符串旋转）用于更改文本颜色和旋转。

这里有些例子。

## remove color legend and text legend 
corrplot(M, order = "AOE", cl.pos = "n", tl.pos = "n")

## bottom  color legend, diagonal text legend, rotate text label
corrplot(M, order = "AOE", cl.pos = "b", tl.pos = "d", tl.srt = 60)

## a wider color legend with numbers right aligned
corrplot(M, order = "AOE", cl.ratio = 0.2, cl.align = "r")

## text labels rotated 45 degrees
corrplot(M, type = "lower", order = "hclust", tl.col = "black", tl.srt = 45)

处理非相关矩阵

corrplot(abs(M),order = "AOE", col = col3(200), cl.lim = c(0, 1))

## visualize a  matrix in [-100, 100]
ran <- round(matrix(runif(225, -100,100), 15))
corrplot(ran, is.corr = FALSE, method = "square")

## a beautiful color legend 
corrplot(ran, is.corr = FALSE, method = "ellipse", cl.lim = c(-100, 100))

如果矩阵是矩形，则可以使用win.asp参数调整纵横比，以使矩阵呈现为正方形。

ran <- matrix(rnorm(70), ncol = 7)
corrplot(ran, is.corr = FALSE, win.asp = .7, method = "circle")

处理缺失（NA）值

默认情况下，corrplot将NA值呈现为"?"字符。使用na.label 参数，可以使用不同的值（最多支持两个字符）。

M2 <- M
diag(M2) = NA
corrplot(M2)

corrplot(M2, na.label = "o")

corrplot(M2, na.label = "NA")

在标签中使用“ plotmath”表达式

从version开始0.78，可以在变量名称中使用 plotmath表达式。要激活plotmath渲染，前缀的人物之一的标签":"，"="或"$"。

M2 <- M[1:5,1:5]
colnames(M2) <- c("alpha", "beta", ":alpha+beta", ":a[0]", "=a[beta]")
rownames(M2) <- c("alpha", "beta", NA, "$a[0]", "$ a[beta]")
corrplot(M2)

将相关图与显着性检验相结合

res1 <- cor.mtest(mtcars, conf.level = .95)
res2 <- cor.mtest(mtcars, conf.level = .99)

## specialized the insignificant value according to the significant level
corrplot(M, p.mat = res1$p, sig.level = .2)

corrplot(M, p.mat = res1$p, sig.level = .05)

corrplot(M, p.mat = res1$p, sig.level = .01)

## leave blank on no significant coefficient
corrplot(M, p.mat = res1$p, insig = "blank")

## add p-values on no significant coefficient
corrplot(M, p.mat = res1$p, insig = "p-value")

## add all p-values
corrplot(M, p.mat = res1$p, insig = "p-value", sig.level = -1)

## add cross on no significant coefficient 
corrplot(M, p.mat = res1$p, order = "hclust", insig = "pch", addrect = 3)

可视化置信区间

corrplot(M, low = res1$lowCI, upp = res1$uppCI, order = "hclust",
         rect.col = "navy", plotC = "rect", cl.pos = "n")

corrplot(M, p.mat = res1$p, low = res1$lowCI, upp = res1$uppCI,
         order = "hclust", pch.col = "red", sig.level = 0.01,
         addrect = 3, rect.col = "navy", plotC = "rect", cl.pos = "n")

res1 <- cor.mtest(mtcars, conf.level = .95)

corrplot(M, p.mat = res1$p, insig = "label_sig",
         sig.level = c(.001, .01, .05), pch.cex = .9, pch.col = "white")

corrplot(M, p.mat = res1$p, method = "color",
         insig = "label_sig", pch.col = "white")

corrplot(M, p.mat = res1$p, method = "color", type = "upper",
         sig.level = c(.001, .01, .05), pch.cex = .9,
         insig = "label_sig", pch.col = "white", order = "AOE")

corrplot(M, p.mat = res1$p, insig = "label_sig", pch.col = "white",
         pch = "p<.05", pch.cex = .5, order = "AOE")

自定义相关图

# matrix of the p-value of the correlation
p.mat <- cor.mtest(mtcars)$p
head(p.mat[, 1:5])

##              [,1]         [,2]         [,3]         [,4]         [,5]
## [1,] 0.000000e+00 6.112687e-10 9.380327e-10 1.787835e-07 1.776240e-05
## [2,] 6.112687e-10 0.000000e+00 1.802838e-12 3.477861e-09 8.244636e-06
## [3,] 9.380327e-10 1.802838e-12 0.000000e+00 7.142679e-08 5.282022e-06
## [4,] 1.787835e-07 3.477861e-09 7.142679e-08 0.000000e+00 9.988772e-03
## [5,] 1.776240e-05 8.244636e-06 5.282022e-06 9.988772e-03 0.000000e+00
## [6,] 1.293959e-10 1.217567e-07 1.222320e-11 4.145827e-05 4.784260e-06

# Specialized the insignificant value according to the significant level
corrplot(M, type = "upper", order = "hclust", 
         p.mat = p.mat, sig.level = 0.01)

# Leave blank on no significant coefficient
corrplot(M, type = "upper", order = "hclust", 
         p.mat = p.mat, sig.level = 0.01, insig = "blank")

在上图中，p值> 0.01的相关被认为是无关紧要的。在这种情况下，相关系数值留为空白或添加叉号。

col <- colorRampPalette(c("#BB4444", "#EE9988", "#FFFFFF", "#77AADD", "#4477AA"))
corrplot(M, method = "color", col = col(200),
         type = "upper", order = "hclust", number.cex = .7,
         addCoef.col = "black", # Add coefficient of correlation
         tl.col = "black", tl.srt = 90, # Text label color and rotation
         # Combine with significance
         p.mat = p.mat, sig.level = 0.01, insig = "blank", 
         # hide correlation coefficient on the principal diagonal
         diag = FALSE)

注意：其中一些情节摘自该博客。

探索大型功能矩阵

# generating large feature matrix (cols=features, rows=samples)
num_features <- 60 # how many features
num_samples <- 300 # how many samples
DATASET <- matrix(runif(num_features * num_samples),
               nrow = num_samples, ncol = num_features)

# setting some dummy names for the features e.g. f23
colnames(DATASET) <- paste0("f", 1:ncol(DATASET))

# let's make 30% of all features to be correlated with feature "f1"
num_feat_corr <- num_features * .3
idx_correlated_features <- as.integer(seq(from = 1,
                                          to = num_features,
                                          length.out = num_feat_corr))[-1]
for (i in idx_correlated_features) {
  DATASET[,i] <- DATASET[,1] + runif(num_samples) # adding some noise
}

corrplot(cor(DATASET), diag = FALSE, order = "FPC",
         tl.pos = "td", tl.cex = 0.5, method = "color", type = "upper")

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R Corrplot软件包简介,绘制相关热图

Corrplot软件包简介介绍所述corrplot包是相关矩阵，置信区间的图形显示。它还包含一些进行矩阵重新排序的算法。另外，corrplot擅长细节，包括选择颜色，文本标签，颜色标签，布局等。可视化方法有七个可视化方法（参数method中）corrplot包，命名"circle"，"square"，"ellipse"，"number"，"shade"，"color"，"pie"。...
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