Arrange Microscopic images in table for publication - r

Question

I wonder if there is an automated way to align several microscopic images together in R to appear in such form like this image (source: doi: https://doi.org/10.1101/2019.12.11.873471). I am not looking for image analysis, only grid the images and add labels. I tried with magick in which I was able to write labels on the images and with gridExtra to align them and add the labels outside. but still not satisfied because I wasn't able to control the distance between the blocks and add labels in boxes like the image above.
can anybody recommend a package to do something like this ( maybe in R or Python, not sure if Latex can do something like that also?).
below is my reproducible code and what I get.
Many thanks for your help.
library(magick)
library(grid)
library(gridExtra)
names_of_images <- LETTERS[1:16]
pic_url <- "https://imagehost.imageupload.net/2020/04/30/EXAMPLE.jpg"
pic_cat <- tempfile()
download.file(pic_url,pic_cat,mode="wb")
pic <- image_read(pic_cat)
## write labels on images
image_listall <- list()
for ( i in names_of_images ) {
im_read_bor <- image_border(pic , 'white' ,geometry = "10x10")
im_read_bor_anno <- image_annotate(im_read_bor, paste(i),
size = 100, color = "white" , location = "+50+40" )
image_listall[[i]] = im_read_bor_anno
}
## arrange images in rows
row1 <- image_append(c(image_listall$A, image_listall$B ,image_listall$C,image_listall$D ), stack = F)
row2 <- image_append(c(image_listall$E, image_listall$F ,image_listall$G,image_listall$H ), stack = F)
row3 <- image_append(c(image_listall$I, image_listall$J,image_listall$K,image_listall$L) ,stack = F)
row4 <- image_append(c(image_listall$M, image_listall$N,image_listall$O, image_listall$P) ,stack = F)
## now add row labels and title
r1 <- grid.arrange(rasterGrob(row1) , top = textGrob(
"First Block",just = "center",
gp = gpar(fontface = 'bold', fontsize = 18)) ,
left = textGrob(
"(A)",
gp = gpar(fontface = 'bold', fontsize = 15)))
r2 <- grid.arrange(rasterGrob(row2) ,
left = textGrob(
"(B)",
gp = gpar(fontface = 'bold', fontsize = 15)))
r3 <- grid.arrange(rasterGrob(row3) , top = textGrob(
"Second Block", just = "center",
gp = gpar(fontface = 'bold', fontsize = 18)) ,
left = textGrob(
"(C)",
gp = gpar(fontface = 'bold', fontsize = 15)))
r4 <- grid.arrange(rasterGrob(row4) ,
left = textGrob(
"(D)",
gp = gpar(fontface = 'bold', fontsize = 15)))
## draw all together
grid.draw(rbind(r1, r2,r3,r4, size = "last"))
it looks like this:

Answer 1

Maybe not the best and more elegant solution, but a possible way will be to use the function facet_grid from ggplot2 to draw multipanel plot. The advantage of using ggplot2 will be that you can benefit for a large panel of tools pretty easy to use to customize the location, the font, the color of all your labels.
So, you can prepare a fake dataframe with your text for each vertical and horizontal label:
verticallabel <- c("Control", "cKO")
horizontallabel <- c("Text1","Text2","Text3")
text <- expand.grid(verticallabel,horizontallabel)
text <- as.data.frame(text)
Var1 Var2
1 Control Text1
2 cKO Text1
3 Control Text2
4 cKO Text2
5 Control Text3
6 cKO Text3
Then, you can create an empty plot with 6 panels with both horizontal and vertical labeling as follow:
library(ggplot2)
g <- ggplot(text, aes(x = Var1, y = Var2))+geom_point(color = NA)+
facet_grid(Var1~Var2, switch = "y")+ labs(tag = "A")+
theme(strip.background = element_blank(),
strip.text = element_blank(),
axis.text = element_blank(),
axis.title = element_blank(),
panel.background = element_blank(),
axis.ticks = element_blank(),
plot.margin = margin(1,1,1,1, unit = "cm"),
plot.tag.position = c(-0.015, 1.05))+
coord_cartesian(clip = "off", ylim = c(0,5), xlim = c(0,2))+
geom_text(data = subset(text, Var1 == "Control"), aes(label = Var2, x = 1, y = 6.3, color = Var2), show.legend = FALSE,vjust = 0.5)+
geom_text(data = subset(text, Var2 == "Text1"), aes(label = Var1, x = -0.8, y = 2.5, angle = 90, vjust = 0))+
geom_rect(data = subset(text, Var1 == "Control"), aes(xmin = -Inf, xmax = Inf, ymax = 6.8, ymin = 5.8), fill = NA, color = "black")+
geom_rect(data = subset(text, Var2 == "Text1"), aes(ymin = -Inf, ymax = Inf, xmin = -1, xmax = -0.7), fill = NA, color = "black")
Then, if you want to add image on each panel, you can use the excellent solution proposed by #EdgarSantos in this post: Adding custom images to ggplot facets
annotation_custom2 <-
function (grob, xmin = -Inf, xmax = Inf, ymin = -Inf, ymax = Inf, data){ layer(data = data, stat = StatIdentity, position = PositionIdentity,
geom = ggplot2:::GeomCustomAnn,
inherit.aes = TRUE, params = list(grob = grob,
xmin = xmin, xmax = xmax,
ymin = ymin, ymax = ymax))}
And here with some example images (some are downloaded on my computer, so you need to adapt path for your images):
library(png)
img1 = readPNG(getURLContent('https://cdn2.iconfinder.com/data/icons/animals/48/Turtle.png'))
img2 = readPNG(getURLContent('https://cdn2.iconfinder.com/data/icons/animals/48/Elephant.png'))
img3 = readPNG(getURLContent('https://cdn2.iconfinder.com/data/icons/animals/48/Hippopotamus.png'))
rlogo <- readPNG("../external-content.duckduckgo.com.png")
rstudio <- readPNG("../rstudio.png")
g +
annotation_custom2(rasterGrob(img1, width =unit(1,"npc"), height = unit(1,"npc")),
xmin = -Inf, xmax =Inf, ymin = -Inf, ymax = Inf, data = text[1,])+
annotation_custom2(rasterGrob(img2, width =unit(1,"npc"), height = unit(1,"npc")),
xmin = -Inf, xmax =Inf, ymin = -Inf, ymax = Inf, data = text[2,])+
annotation_custom2(rasterGrob(img3, width =unit(1,"npc"), height = unit(1,"npc")),
xmin = -Inf, xmax =Inf, ymin = -Inf, ymax = Inf, data = text[3,])+
annotation_custom2(rasterGrob(rlogo, width =unit(1,"npc"), height = unit(1,"npc")),
xmin = -Inf, xmax =Inf, ymin = -Inf, ymax = Inf, data = text[4,])+
annotation_custom2(rasterGrob(rstudio, width =unit(1,"npc"), height = unit(1,"npc")),
xmin = -Inf, xmax =Inf, ymin = -Inf, ymax = Inf, data = text[5,])
Does it answer your question ?