标签: cowplot

我有heatmap(来自一组样本的基因表达):

set.seed(10)
mat <- matrix(rnorm(24*10,mean=1,sd=2),nrow=24,ncol=10,dimnames=list(paste("g",1:24,sep=""),paste("sample",1:10,sep="")))
dend <- as.dendrogram(hclust(dist(mat)))
row.ord <- order.dendrogram(dend)
mat <- matrix(mat[row.ord,],nrow=24,ncol=10,dimnames=list(rownames(mat)[row.ord],colnames(mat)))
mat.df <- reshape2::melt(mat,value.name="expr",varnames=c("gene","sample"))

require(ggplot2)
map1.plot <- ggplot(mat.df,aes(x=sample,y=gene))+geom_tile(aes(fill=expr))+scale_fill_gradient2("expr",high="darkred",low="darkblue")+scale_y_discrete(position="right")+
  theme_bw()+theme(plot.margin=unit(c(1,1,1,-1),"cm"),legend.key=element_blank(),legend.position="right",axis.text.y=element_blank(),axis.ticks.y=element_blank(),panel.border=element_blank(),strip.background=element_blank(),axis.text.x=element_text(angle=45,hjust=1,vjust=1),legend.text=element_text(size=5),legend.title=element_text(size=8),legend.key.size=unit(0.4,"cm"))

(由于plot.margin我正在使用的论据,左侧被切断,但我需要这个,如下所示).

然后,我prune行dendrogram根据深度截止值来获得较少的集群(即,只有深深的分裂),并做一些编辑所产生dendrogram有它绘制他们的方式,我希望它:

depth.cutoff <- 11
dend <- cut(dend,h=depth.cutoff)$upper
require(dendextend)
gg.dend <- as.ggdend(dend)
leaf.heights <- dplyr::filter(gg.dend$nodes,!is.na(leaf))$height
leaf.seqments.idx <- which(gg.dend$segments$yend %in% leaf.heights)
gg.dend$segments$yend[leaf.seqments.idx] <- max(gg.dend$segments$yend[leaf.seqments.idx])
gg.dend$segments$col[leaf.seqments.idx] <- "black"
gg.dend$labels$label <- 1:nrow(gg.dend$labels)
gg.dend$labels$y <- max(gg.dend$segments$yend[leaf.seqments.idx])
gg.dend$labels$x <- gg.dend$segments$x[leaf.seqments.idx]
gg.dend$labels$col <- "black"
dend1.plot <- ggplot(gg.dend,labels=F)+scale_y_reverse()+coord_flip()+theme(plot.margin=unit(c(1,-3,1,1),"cm"))+annotate("text",size=5,hjust=0,x=gg.dend$label$x,y=gg.dend$label$y,label=gg.dend$label$label,colour=gg.dend$label$col)

我用cowplot's将它们绘制在一起plot_grid:

require(cowplot)
plot_grid(dend1.plot,map1.plot,align='h',rel_widths=c(0.5,1)) …

我正试图通过使用cowplot包来以出版物的方式安排绘图.
我只是希望面板的尺寸和尺寸相同.

可重复的示例

library(ggplot2)
library(cowplot)

gg1 <- ggplot(mtcars)+
        geom_point(aes(x=mpg,y=hp))+
        theme_bw()+
        theme(aspect.ratio=1)

gg2 <- ggplot(mtcars)+
        geom_point(aes(x=mpg,y=hp,fill=cyl))+
        facet_wrap(~cyl,ncol=2)+
        theme_bw()+
        theme(aspect.ratio=1,
              legend.position='none')

output <- plot_grid(gg1,gg2, labels = c('A','B'),label_size = 20)
print(output)

代码生成此图.

如您所见,水平轴既不匹配,也不匹配面板的上边缘.

这个论点align从cowplot不方位图工作.

有任何想法吗？

我最近安装了这个cowplot包.然而,在这样做之后,我注意到我的ggplots缺少他们的背景和网格线theme_grey()!

创建上述每个图的代码是:

result_df %>%
    ggplot(aes_string(x = 'p', y = 'r')) +
    # theme_grey() + # uncomment this line to produce plot on right
    geom_point(aes(group = c), size = 0.5) +
    geom_line(aes(group = c), size = 0.2, linetype = 'dotted') +
    theme(axis.text.x=element_text(angle = 90, hjust = 1, vjust = 0.5)) +
    facet_grid(b ~ e, scales = "free_y") +
    scale_x_continuous(breaks = seq(0, 10, 2))

没有明确调用+ theme_grey(),我得到左边的情节.

这里发生了什么？我以为那theme_grey()是默认的.如何查看我的默认主题是什么？

这是我的一个片段sessionInfo():

R version 3.3.2 (2016-10-31) …

该ggplot2附加软件包,cowplot具有用来绘制多条曲线称为一个不错的功能plot_grid().这是plot_grid()在行动:

library(ggplot2); library(cowplot)

plot_a <- ggplot(mtcars, aes(mpg, wt)) + geom_point()
plot_b <- ggplot(mtcars, aes(mpg, disp)) + geom_point()

plot_grid(plot_a, plot_b, labels = c("A", "B"))

但请注意加载如何cowplot更改默认的绘图样式.如何加载cowplot包以便我可以使用该plot_grid()功能,但也禁用cowplot强制执行的默认打印样式？

这是我的代码：

library(ggplot2)
library(cowplot)


df <- data.frame(
  x = 1:10, y1 = 1:10, y2 = (1:10)^2, y3 = (1:10)^3, y4 = (1:10)^4
)

p1 <- ggplot(df, aes(x, y1)) + geom_point()
p2 <- ggplot(df, aes(x, y2)) + geom_point()
p3 <- ggplot(df, aes(x, y3)) + geom_point()
p4 <- ggplot(df, aes(x, y4)) + geom_point()
p5 <- ggplot(df, aes(x, y3)) + geom_point()
# simple grid
plot_grid(p1, p2, 
          p3, p4,
          p5, p4)

但我不想重复p4我想“拉伸”p4以占据col2以及第2行和第3行。

有什么帮助吗？

我刚刚用包构建了一个网格cowplot(用来标记AD的图).这些地块是用包装制成的ggplot2:

pfour<-ggplot(four, aes(x=Concentration, y=Percentage, fill=Phenotype)) + 
 geom_bar(stat='identity',color='black') +
 scale_fill_grey(start = .4, end = .9) + 
 theme_bw()+ylab("Distribution") + 
 xlab("Contentration [mg/ml]") + 
 ggtitle("96 hpf") +
 theme(legend.title = element_text(colour="black", size=10, face="bold")) +
 theme(legend.background = element_rect(fill="white",
                                        size=0.5, linetype="solid", 
                                        colour ="black")) +
 scale_x_discrete(limits=c('uninjected','control','0.002', '0.02', '0.2'),
                  labels=c('uninjected\n(n=251)',
                           'control\n(n=248)', 
                           '0.002\n(n=205)', 
                           '0.02\n(n=222)', 
                           '0.2\n(n=203)'))

数据看起来像那样(4个不同的表,百分比略有不同但原理相同):

Concentration,Percentage,Phenotype
uninjected,0.996015936,0
uninjected,0,1
uninjected,0.003984064,2
uninjected,0,3
uninjected,0,4
control,0.995967742,0
control,0.004032258,1
control,0,2
control,0,3
control,0,4
0.002,0.985365854,0
0.002,0.004878049,1
0.002,0.004878049,2
0.002,0,3
0.002,0.004878049,4
0.02,0.981981982,0
0.02,0.004504505,1
0.02,0.004504505,2
0.02,0.004504505,3
0.02,0.004504505,4
0.2,0.985221675,0
0.2,0.004926108,1
0.2,0,2

它看起来像那样:

代码是:

plot_grid(ponezoom, ptwozoom,pthreezoom,pfourzoom, align='h', labels=c('A', …

从昨天开始,我正在阅读答案和网站,以便在一个图表中合并和对齐,histogram并boxplot使用ggplot2包生成.

这个问题与其他问题不同,因为boxplot chart需要减少在左边缘height和aligned左边缘histogram.

考虑以下数据集:

my_df <- structure(list(id = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 
12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 
28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 
44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, …

我正在尝试在两个与plot_grid牛皮画包装对齐的地块周围绘制边框.请参阅以下示例(从"更改轴位置"晕影修改):

require(gtable)
require(cowplot)

# top plot
p1 <- ggplot(mtcars, aes(mpg, disp)) + geom_line(colour = 'blue') +
  background_grid(minor = 'none')
g1 <- switch_axis_position(p1, 'xy') # switch both axes
g1 <- gtable_squash_rows(g1, length(g1$height)) # set bottom row to 0 height

# bottom plot
p2 <- ggplot(mtcars, aes(mpg, qsec)) + geom_line(colour = 'green') + ylim(14, 25) +
  background_grid(minor = 'none')
g2 <- ggplotGrob(p2)
g2 <- gtable_add_cols(g2, g1$widths[5:6], 4) # add the two additional columns that g1 has
g2 <- …

我正在用ggplot2绘制热图。y轴上的几个刻度需要标记。但是，其中一些过于紧密和重叠。我知道ggrepel可以分隔文本标签，但是目前我还没有解决我的问题。

我的代码如下。任何建议都欢迎。谢谢。

码：

df <- data.frame()

for (i in 1:50){
  tmp_df <- data.frame(cell=paste0("cell", i), 
                       gene=paste0("gene", 1:100), exp = rnorm(100), ident = i %% 5)
  df<-rbind(df, tmp_df)
}

labelRow=rep("", 100)
for (i in c(2, 5, 7, 11, 19, 23)){
  labelRow[i] <- paste0("gene", i)
}

library(ggplot2)
heatmap <- ggplot(data = df, mapping = aes(x = cell, y = gene, fill = exp)) +
  geom_tile() + 
  scale_fill_gradient2(name = "Expression") + 
  scale_y_discrete(position = "right", labels = labelRow) +
  facet_grid(facets = ~ident,
             drop = TRUE, …

我正在尝试创建一个结合了 2 个独立图例和多个绘图网格的绘图。我遇到的问题是我发现很难对齐图例以使它们可见且不重叠。希望下面的例子能够解释我的意思。

首先，我将创建 2 个图。在这两个图中，我只对图例感兴趣，并且我放弃了实际的图（所以请忽略这两个图中的实际图）。为了获得图例，我正在使用该cowplot包。

library(ggplot2)
library(cowplot)
# -------------------------------------------------------------------------
# plot 1 ------------------------------------------------------------------

# create fake data
dfLegend_1 <- data.frame(x = LETTERS[1:10], y = c(1:10))
# set colours
pointColours <- c(A = "#F5736A", B = "#D58D00", C = "#A0A300",
                  D = "#36B300", E = "#00BC7B", F = "#00BCC2",
                  G = "#00ADF4", H = "#928DFF", I = "#E568F0",
                  J = "#808080")

# plot
ggLegend_1 <- ggplot(dfLegend_1, aes(x=x, y=y))+
  geom_point(aes(fill = pointColours), shape = 22, size = 10) + …