geom_bar：颜色渐变和交叉阴影（使用gridSVG），透明度问题 [英] geom_bar: color gradient and cross hatches (using gridSVG), transparency issue
问题描述
使用真棒 ggplot 包，我想要一个barplot，其中<code> fill 审美性被映射到一个连续变量，实际上是q值，最重要的是纹理，实际上是条纹和交叉线。
颜色渐变很重要，因为它代表重要性，而纹理会显示类别A ，B和它们的重叠。所以对角线分别以一种方式，相反的方式和交叉线。
我知道一个维恩图可以完成这项工作，但是我们有35个样本，比较起来我会更容易看出来。
fill 是微不足道的，但是，纹理很棘手。在SO上，感谢。我几乎认为完全使用 d3 或者基于`d3建立的库
< code library（ggplot2）
library（gridSVG）
library（gridExtra）
library（dplyr）
library（RColorBrewer ）
$ b $ 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，重叠，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，color =black，stat =identity，position =stack，alpha = 1）+
ylim（c（0,2000））+
theme_classic（18）+
主题（panel.grid.major = element_line（color =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），colors = cols，limits = c（0，20））
＃使用svglite和htmltools
library（svglite）
library（htmltools）
$ b $将svg作为标记
pso_svg< - htmlSVG（print（pso） ，高度= 10，宽度= 14）
可浏览（
attachDependencies（
tagList（
（
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（））; $如果（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
）
）
）
）
Using the awesome ggplot package, I want a barplot where the fill aesthetic is mapped to a continous variable, actually qvalues and on top of it a texture, actually stripes and cross hatches.
The colour gradient is important because it represents significance while the texture would show the category, "A", "B", and their overlap. So diagonals in one way, the opposite way and cross hatches respectively. I know a Venn diagram could do the job, but we 35 samples and the comparison will be easier to see I think.
The fill is trivial, however, the texture one is tricky. On SO, thanks to @baptise (see here and here) I managed to get this output with dummy data:
The issue is the transparency of the crosses's background. If it is possible get the alpha working on the background in the grid.patternFill() function that would be great. Unfortunately, in my hands it doesn't work.
Any help will be much appreciated.
dummy data can loaded here:
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"))
Code is here:
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()
In grid.patternFill the alpha parameter is suppose to give the transparency, as far as I understood it. But, it has no effect, and the colour is lost. I filled the patterns only for the first bar so you see the contrast.
Edit: the alpha is working fine, but it acts on the pattern itself, i.e the lines. That explains why the lines appear so pale. The issue is more that the background is assumed white and without transparency.
The linetype mapping was a attempt to highlight the overlap part, but it is not nice. If the transparency works for gridSVG I will discard this part and keep a solid line all the way.
Many thanks in advance,
Aurelien
If of any use, output of 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
This really is not an answer, but I will provide this following code as reference for someone who might like to see how we might accomplish this task. A live version is here. I almost think it would be easier to do entirely with d3 or library built on `d3
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"
)
)
)
)
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