r中的绘图板布局热图

Question

I am trying to plot a plate layout heatmap in R. The plate layout is simply 8 (row) x 12 (column) circles (wells). Rows are labeled by alphabets and columns by numbers. Each well need to be filled with some color intensity depends upon a qualitative or quantitative variable. The plate layout look like this:

Here is small dataset:

 set.seed (123)
platelay <- data.frame (rown = rep (letters[1:8], 12), coln = rep (1:12, each = 8),
colorvar = rnorm (96, 0.3, 0.2))

   rown coln     colorvar
1     a    1  0.187904871
2     b    1  0.253964502
3     c    1  0.611741663
4     d    1  0.314101678
5     e    1  0.325857547
6     f    1  0.643012997
7     g    1  0.392183241
8     h    1  0.046987753
9     a    2  0.162629430
10    b    2  0.210867606
11    c    2  0.544816359
12    d    2  0.371962765
13    e    2  0.380154290
14    f    2  0.322136543
15    g    2  0.188831773
16    h    2  0.657382627
17    a    3  0.399570096
18    b    3 -0.093323431
19    c    3  0.440271180
20    d    3  0.205441718
21    e    3  0.086435259
22    f    3  0.256405017
23    g    3  0.094799110
24    h    3  0.154221754
25    a    4  0.174992146
26    b    4 -0.037338662
27    c    4  0.467557409
28    d    4  0.330674624
29    e    4  0.072372613
30    f    4  0.550762984
31    g    4  0.385292844
32    h    4  0.240985703
33    a    5  0.479025132
34    b    5  0.475626698
35    c    5  0.464316216
36    d    5  0.437728051
37    e    5  0.410783531
38    f    5  0.287617658
39    g    5  0.238807467
40    h    5  0.223905800
41    a    6  0.161058604
42    b    6  0.258416544
43    c    6  0.046920730
44    d    6  0.733791193
45    e    6  0.541592400
46    f    6  0.075378283
47    g    6  0.219423033
48    h    6  0.206668929
49    a    7  0.455993024
50    b    7  0.283326187
51    c    7  0.350663703
52    d    7  0.294290649
53    e    7  0.291425909
54    f    7  0.573720457
55    g    7  0.254845803
56    h    7  0.603294121
57    a    8 -0.009750561
58    b    8  0.416922750
59    c    8  0.324770849
60    d    8  0.343188314
61    e    8  0.375927897
62    f    8  0.199535309
63    g    8  0.233358523
64    h    8  0.096284923
65    a    9  0.085641755
66    b    9  0.360705728
67    c    9  0.389641956
68    d    9  0.310600845
69    e    9  0.484453494
70    f    9  0.710016937
71    g    9  0.201793767
72    h    9 -0.161833775
73    a   10  0.501147705
74    b   10  0.158159847
75    c   10  0.162398277
76    d   10  0.505114274
77    e   10  0.243045399
78    f   10  0.055856458
79    g   10  0.336260696
80    h   10  0.272221728
81    a   11  0.301152837
82    b   11  0.377056080
83    c   11  0.225867994
84    d   11  0.428875310
85    e   11  0.255902688
86    f   11  0.366356393
87    g   11  0.519367803
88    h   11  0.387036298
89    a   12  0.234813683
90    b   12  0.529761524
91    c   12  0.498700771
92    d   12  0.409679392
93    e   12  0.347746347
94    f   12  0.174418785
95    g   12  0.572130490
96    h   12  0.179948083

Is there is package that can readily do it ? Is it possible write a function in base or ggplot2 or other package that can achieve this target.

Answer 1

Changing the colour of points of sufficient size, with ggplot2 . Note I've implemeted @TylerRinkler's suggestion, but within the call to ggplot . I've also removed the axis labels

ggplot(platelay, aes(y = factor(rown, rev(levels(rown))),x = factor(coln))) + 
     geom_point(aes(colour = colorvar), size =18)  +theme_bw() +
     labs(x=NULL, y = NULL)

And a base graphics approach, which will let you have the x axis above the plot

# plot with grey colour dictated by rank, no axes or labels
with(platelay, plot( x=as.numeric(coln), y= rev(as.numeric(rown)), pch= 19, cex = 2, 
 col = grey(rank(platelay[['colorvar']] ) / nrow(platelay)), axes = F, xlab= '', ylab = ''))
# add circular outline
with(platelay, points( x=as.numeric(coln), y= rev(as.numeric(rown)), pch= 21, cex = 2))
# add the axes
axis(3, at =1:12, labels = 1:12)
axis(2, at = 1:8, labels = LETTERS[8:1])
# the background grid
grid()
# and a box around the outside
box()

Answer 2

And for giggles and Christmas cheer, here is a version using base R plotting functions. Though there is very possibly a better solution.

dev.new(width=6,height=4)

rown <- unique(platelay$rown)
coln <- unique(platelay$coln)

plot(NA,ylim=c(0.5,length(rown)+0.5),xlim=c(0.5,length(coln)+0.5),ann=FALSE,axes=FALSE)
box()

axis(2,at=seq_along(rown),labels=rev(rown),las=2)
axis(3,at=seq_along(coln),labels=coln)

colgrp <- findInterval(platelay$colorvar,seq(min(platelay$colorvar),max(platelay$colorvar),length.out=10))
colfunc <- colorRampPalette(c("green", "blue"))
collist <- colfunc(length(unique(colgrp))) 

symbols(platelay$coln,
        factor(platelay$rown, rev(levels(platelay$rown))),
        circles=rep(0.2,nrow(platelay)),
        add=TRUE,
        inches=FALSE,
        bg=collist[colgrp])

And the resulting image:

Answer 3

here a solution using ggplot2 solution of @mnel and grid solution

here the code of given solution

d <- ggplot(platelay, aes(y=rown,x=factor(coln))) + 
  geom_point(aes(colour = colorvar), size =18) + theme_bw()

I use the data generated by ggplot

data <- ggplot_build(d)$data[[1]]

 x <- data$x
 y <- data$y
 grid.newpage()
 pushViewport(plotViewport(c(4, 4, 2, 2)),
               dataViewport(x, y))

grid hase an ellipse geom

 grid.ellipse(x, y,size=20,  ar = 2,angle=0,gp =gpar(fill=data$colour))
 grid.xaxis(at=c(labels=1:12,ticks=NA),gp=gpar(cex=2))
 grid.yaxis(at = 1:8,label=rev(LETTERS[1:8]),gp=gpar(cex=2))

 grid.roundrect(gp=gpar(fill=NA))

I add grid :

gpgrid <- gpar(col='grey',lty=2,col='white')
grid.segments(unit(1:12, "native") ,unit(0, "npc"), unit(1:12, "native"),unit(1, "npc"),gp=gpgrid)
grid.segments(unit(0, "npc"), unit(1:8, "native"), unit(1, "npc"),unit(1:8, "native"),gp=gpgrid)
upViewport()

Answer 4

This answer is an add on for @thelatemail answer which explains the platemap for (8,12) = 96 format.

To construct (32,48) = 1536 format, single digits of AZ is insufficent. Hence one needs to expand letters such as AA, AB, AC, AD ... ZZ and it can be expanded to three or more digits by concatenating LETTERS to the levels variable as below.

levels = c(LETTERS, c(t(outer(LETTERS, LETTERS, paste, sep = "")))))

@thelatemail answer can be improved for letters in double digits for 1536 plate format as below

rown = rep (c(LETTERS, c(t(outer(LETTERS[1], LETTERS[1:6], paste, sep = "")))),

symbols(platelay$coln,
        factor(platelay$rown, 
               levels = rev(c(LETTERS, c(t(outer(LETTERS[1], LETTERS[1:6], paste, sep = "")))))),
        circles=rep(0.45,nrow(platelay)),
        add=TRUE,
        inches=FALSE,
        bg=collist[colgrp])

The levels variable inside symbols function should have characters with alphabetically sorted single, then double, then triple ... and so on digits.

For example, if you have below incorrect order of levels inside the symbols function, then it will plot with incorrect color representation.

Incorrect order: A, AA, AB, AC, AD, AE, AF, B, C,D, ...Z

Correct order: A, B, C, D, E, .....Z, AA, AB, AC, AD, AE, AF