Question

使用令人敬畏的ggplot包，我想要一个条形图，其中fill美学被映射到一个连续变量，实际上是qvalues，在它上面是一个纹理，实际上是条纹和交叉阴影。

颜色渐变很重要，因为它代表重要性，而纹理则显示类别“A”，“B”及其重叠。所以对角线分别以一种方式，相反的方式和交叉的阴影线。我知道维恩图可以完成这项工作，但我认为我们更容易看到35个样本和比较。

fill是微不足道的，然而，纹理是棘手的。在SO上，感谢@baptise（请参阅here和here），我设法使用虚拟数据获取此输出： crossbars

问题是十字架背景的透明度。如果有可能让alpha在grid.patternFill()函数的背景上工作，那就太棒了。不幸的是，在我手中它不起作用。

非常感谢任何帮助。

可以在此处加载虚拟数据：

dfso <- structure(list(Sample = c("S1", "S2", "S1", "S2", "S1", "S2"), 
  qvalue = c(14.704287341, 8.1682824035, 13.5471896224, 6.71158432425, 
  12.3900919038, 5.254886245), type = structure(c(1L, 1L, 2L, 
  2L, 3L, 3L), .Label = c("A", "overlap", "B"), class = "factor"), 
  value = c(897L, 1082L, 503L, 219L, 388L, 165L)), class = c("tbl_df", 
  "tbl", "data.frame"), row.names = c(NA, -6L), .Names = c("Sample", 
  "qvalue", "type", "value"))

代码在这里：

library("ggplot2")
library("gridSVG")
library("gridExtra")
library("dplyr")
library("RColorBrewer")

cols <- brewer.pal(7,"YlOrRd")
pso <- ggplot(dfso)+
  geom_bar(aes(x = Sample, y = value, fill = qvalue, linetype = type), width = .8, colour = "black", stat = "identity", position = "stack", alpha = 1)+
  theme_classic(18)+
  theme( panel.grid.major = element_line(colour = "grey80"),
     panel.grid.major.x = element_blank(),
     panel.grid.minor = element_blank(),
     legend.key = element_blank(),
     axis.text.x = element_text(angle = 90, vjust = 0.5))+
  guides(linetype = FALSE) +
  ylab("Count")+
  scale_fill_gradientn("-log10(qvalue)", colours = cols, limits = c(0, 20))+
  scale_linetype_manual(values = c("dotted", "solid", "dotted"))+
  scale_y_continuous(expand = c(0, 0), limits = c(0, 2000))

# gridSVG
pat1 <- pattern(linesGrob(gp = gpar(col="black", lwd = 1)),
                width = unit(5, "mm"), height = unit(5, "mm"),
                dev.width = 1, dev.height = 1)
pat2 <- pattern(linesGrob(x = unit(0:1, "npc"), y = unit(1:0, "npc"),
                          gp = gpar(col="black", lwd = 1)),
                width = unit(5, "mm"), height = unit(5, "mm"),
                dev.width = 1, dev.height = 1)
crossGrob <- gTree(children = gList(linesGrob(gp = gpar(col="black", lwd = 1)), linesGrob(x = unit(0:1, "npc"), y = unit(1:0, "npc"), gp = gpar(col="black", lwd = 1))))
registerPatternFill("hash1", pat1)
registerPatternFill("hash2", pat2)
registerPatternFill("cross", grob = crossGrob, dev.width = 1, dev.height = 1, width = unit(5, "mm"), height = unit(5, "mm"))
gridsvg("crossbars.svg", width = 10)
print(pso)
grid.force()
grid.patternFill("geom_rect.rect", alpha = 0.2, grep = TRUE, group = FALSE,
                 label = rep(c("hash1", "cross", "hash2"), 1))
dev.off()

在grid.patternFill alpha参数中，假设我提供透明度，据我所知。但是，它没有效果，颜色也会丢失。我只为第一个条填充了图案，因此您可以看到对比度。

编辑：alpha工作正常，但它会对模式本身起作用，即这些行。这就解释了为什么线条看起来很苍白。问题更多的是背景被假定为白色而没有透明度。

linetype映射是为了突出显示重叠部分，但这并不好。如果透明度适用于gridSVG，我将丢弃此部分并一直保持实线。

非常感谢，

的Aurelien

如有任何用途，请输出sessionInfo()：

R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin14.3.0 (64-bit)
Running under: OS X 10.10.4 (Yosemite)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] gridExtra_0.9.1    RColorBrewer_1.1-2 dplyr_0.4.1        gridSVG_1.4-3      ggplot2_1.0.1     
loaded via a namespace (and not attached):
 [1] Rcpp_0.11.6      XML_3.98-1.3     assertthat_0.1   digest_0.6.8     MASS_7.3-42      plyr_1.8.3       DBI_0.3.1       
 [8] gtable_0.1.2     magrittr_1.5     scales_0.2.5     stringi_0.5-5    reshape2_1.4.1   labeling_0.3     proto_0.3-10    
[15] RJSONIO_1.3-0    tools_3.2.1      stringr_1.0.0    munsell_0.4.2    parallel_3.2.1   colorspace_1.2-6

Answer 1

我正在回答我自己的问题，因为有一种方法可以将特定的颜色填充到模式中，感谢link。在第一个栏上，对于类别＆＃34; A＆＃34;，它可能如下所示： cross

用以下代码替换pat1模式：

pat1 <- pattern(gTree(children=gList(
                      rectGrob(gp=gpar(col=NA, fill=cols[4])),
                      linesGrob(gp=gpar(col="black", lwd = 5)))),
                      width = unit(5, "mm"), height = unit(5, "mm"),
                      dev.width = 1, dev.height = 1)

对于颜色较少的geom_bar，它会起作用，但对于我的fill颜色映射到热图规模的问题，它将会很乏味。

Answer 2

这不是一个真正的答案，但我会提供以下代码作为参考，以便有人想看看我们如何完成这项任务。实时版本为here。我几乎认为完全使用基于d3

构建的d3或库会更容易

library("ggplot2")
library("gridSVG")
library("gridExtra")
library("dplyr")
library("RColorBrewer")

dfso <- structure(list(Sample = c("S1", "S2", "S1", "S2", "S1", "S2"), 
                       qvalue = c(14.704287341, 8.1682824035, 13.5471896224, 6.71158432425, 
                                  12.3900919038, 5.254886245), type = structure(c(1L, 1L, 2L, 
                                                                                  2L, 3L, 3L), .Label = c("A", "overlap", "B"), class = "factor"), 
                       value = c(897L, 1082L, 503L, 219L, 388L, 165L)), class = c("tbl_df", 
                                                                                  "tbl", "data.frame"), row.names = c(NA, -6L), .Names = c("Sample", 
                                                                                                                                           "qvalue", "type", "value"))

cols <- brewer.pal(7,"YlOrRd")
pso <- ggplot(dfso)+
  geom_bar(aes(x = Sample, y = value, fill = qvalue), width = .8, colour = "black", stat = "identity", position = "stack", alpha = 1)+
  ylim(c(0,2000)) + 
  theme_classic(18)+
  theme( panel.grid.major = element_line(colour = "grey80"),
         panel.grid.major.x = element_blank(),
         panel.grid.minor = element_blank(),
         legend.key = element_blank(),
         axis.text.x = element_text(angle = 90, vjust = 0.5))+
  ylab("Count")+
  scale_fill_gradientn("-log10(qvalue)", colours = cols, limits = c(0, 20))

# use svglite and htmltools
library(svglite)
library(htmltools)

# get the svg as tag
pso_svg <- htmlSVG(print(pso),height=10,width = 14)

browsable(
  attachDependencies(
    tagList(
      pso_svg,
      tags$script(
        sprintf(
"
  var data = %s

  var svg = d3.select('svg');

  svg.select('style').remove();

  var bars = svg.selectAll('rect:not(:last-of-type):not(:first-of-type)')
     .data(d3.merge(d3.values(d3.nest().key(function(d){return d.Sample}).map(data))))

  bars.style('fill',function(d){
    var t = textures
              .lines()
              .background(d3.rgb(d3.select(this).style('fill')).toString());

    if(d.type === 'A') t.orientation('2/8');
    if(d.type === 'overlap') t.orientation('2/8','6/8');
    if(d.type === 'B') t.orientation('6/8');

    svg.call(t);
    return t.url();
  });
"    
          ,
          jsonlite::toJSON(dfso)
        )
      )
    ),
    list(
      htmlDependency(
        name = "d3",
        version = "3.5",
        src = c(href = "http://d3js.org"),
        script = "d3.v3.min.js"
      ),
      htmlDependency(
        name = "textures",
        version = "1.0.3",
        src = c(href = "https://rawgit.com/riccardoscalco/textures/master/"),
        script = "textures.min.js"
      )
    )
  )
)

geom_bar：颜色渐变和交叉阴影（使用gridSVG），透明度问题

2 个答案: