ggh4x
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Published
20 hours ago •
teunbrand
teunbrand
A problem I met about ggh4x after its update from v 0.1.2.1 to v 0.2.1
I draw a plot using ggplot2 and ggh4x with the help from @teunbrand. And it works perfect in ggh4x old version 0.1.2.1. A key function was from the author and it helped me a lot.
But several days ago, I updated some pacages including the ggh4x and now it is v 0.2.1.
Then the plot can not be produced normally with the error: Error in strip$grobs[is_strip][1] : 下标出界(subscript out of bounds)
So I think it may work if I downgrade the ggh4x version to the original version 0.1.2.1.
However the problem stil exists. I haven't changed my data so I want to know if there is something wrong with the ggh4x ?
######## here is the original question: Can I adjust the fill(color) of different label regions when using ggh4x package
Here is the code:
data<-structure(list(Name = structure(53:68, .Label = c("1_control",
"1_CCM(Kit1 ko)", "2_control", "2_CCM(Pdcd20 ko)", "3_control",
"3_1 day", "3_3 days", "3_1 month", "4_control", "4_1 day", "4_3 days",
"4_1 month", "5_control", "5_1 day", "5_3 days", "5_1 month",
"6_control", "6_TBI(1 day)", "7_control", "7_TBI(3 day)", "8_control",
"8_TBI(1 month)", "9_control", "9_VEGF", "10_control", "10_VEGF",
"11_Brain Healty", "12_control_1", "12_control_2", "12_AOD(Jnk1/2/3 ko)",
"13_control", "13_Cpt1_ko(Cdh5 driven)", "14_control", "14_Tsc2ko(Tbx4 driven)",
"15_control", "15_Zmpste24 ko", "16_control", "16_Adrenomedullin\nko(Cdh5 driven)",
"17_Lung Healthy", "18_control(14w)", "18_carboplatin(14w)",
"18_radiation(14w)", "18_6 weeks", "18_70 weeks", "19_ECs(bone marrow)",
"20_control", "20_diabetic nephropathy", "21_control", "21_Alport syndrome",
"22_control", "22_Alport syndrome", "23_Kidney Healthy", "24_control",
"24_Differentiated", "25_Heart Healthy", "26_control", "26_Tumor",
"27_control", "27_Nonalcoholic\nsteatohepatitis", "28_Liver Healthy",
"29_control", "29_autoimmune uveitis", "30_control", "30_facioscapulohumeral\nmuscular dystrophy",
"31_control", "31_RANKL ko", "32_control", "32_Notch1 +/vg",
"32_Notch1 +/12", "32_Notch1 +/-", "32_Notch1 -/12"), class = "factor"),
Disease = structure(c(24L, 24L, 25L, 26L, 26L, 27L, 27L,
28L, 29L, 29L, 30L, 30L, 31L, 31L, 32L, 32L), .Label = c("CCM\nmodel1",
"CCM\nmodel2", "Epilepsy", "EAE", "Stroke", "TBI\n1day",
"TBI\n3day", "TBI\n1month", "VEGF\nsti_DG\nregion", "VEGF\nsti_CA1\nregion",
"Healthy\n(Brain)", "AOD", "CPT1\nko", "Tsc2\nko", "Zmpste\n_24 ko",
"AM\nko", "Healthy\n(Lung)", "Chemo\nRadio\n(Tibiae)", "ECs\n(BM)",
"diabetic\nnephro\n_pathy", "Alport\nsyndrome\nEC\npopulation1",
"Alport\nsyndrome\nEC\npopulation2", "Healthy\n(Kidney)",
"Aorta", "Healthy\n(Heart)", "Tumor", "NASH", "Healthy\n(Liver)",
"EAU", "FSHD", "RANKL\nko", "Notch1\nmodified"), class = "factor"),
Organ = structure(c(5L, 5L, 5L, 6L, 6L, 6L, 6L, 6L, 7L, 7L,
8L, 8L, 9L, 9L, 10L, 10L), .Label = c("Brain", "Lung", "Bone",
"Kidney", "Aorta", "Liver", "Retina", "Mus", "Lymp", "Embryo"
), class = "factor"), fill = c("#FFFFFF", "#FFFF33", "#FFFFFF",
"#FFFFFF", "#00F5FF", "#FFFFFF", "#00F5FF", "#FFFFFF", "#FFFFFF",
"#666666", "#FFFFFF", "#7FC97F", "#FFFFFF", "#BEAED4", "#FFFFFF",
"#A6D854"), Condition = c("#FFFFFF", "#FFFFFF", "#FFFFFF",
"#CCCCFF", "#CCCCFF", "#CCCCFF", "#CCCCFF", "#CCCCFF", "#CCCCFF",
"#CCCCFF", "#CCCCFF", "#CCCCFF", "#fbb03b", "#fbb03b", "#fbb03b",
"#fbb03b"), Organ_fill = c("#FFFF33", "#FFFF33", "#FFFF33",
"#00F5FF", "#00F5FF", "#00F5FF", "#00F5FF", "#00F5FF", "#666666",
"#666666", "#7FC97F", "#7FC97F", "#BEAED4", "#BEAED4", "#A6D854",
"#A6D854"), mean = c(858.98750157615, 420.38122185754, 262.590442373838,
185.670810881339, 233.452076898716, 3219.28563479013, 2427.32556269574,
1552.81582140235, 394.765393523994, 420.454351698853, 1295.47692129111,
1357.53823242958, 1352.71703262044, 1319.89488759262, 4.78327819764262,
6.86013366170554), sd = c(55.535911372066, 15.5347305073907,
29.5537795773611, 17.4390137323828, 36.0381883614951, 641.298872189499,
338.296364941458, 254.748027714364, 17.1375059099585, 100.491982520438,
49.0693043847785, 191.034062908029, 105.031407429784, 185.916546617784,
1.21846060820158, 3.38993644072368)), row.names = 53:68, class = "data.frame")
#####
g <- ggplot(data = data, aes(Name,mean, label = Name,fill=Organ)) +
geom_bar(position="dodge2", stat="identity",width = 0.85,color="black") +
geom_errorbar(aes(ymin = mean - sd, ymax = mean + sd),position = position_dodge(0.85), width = .2) +
facet_nested(.~Organ+Disease, scales="free",switch = "x",nest_line = TRUE)+
theme_classic() +
theme(
plot.title = element_text(hjust = 0.5),
plot.margin = unit(c(5, 10, 10, 10), "mm"),
strip.background = element_rect(colour="black", fill="white"),
strip.text.x = element_text(size = 6, angle=0),
strip.placement = "outside")
# Convert to gtable
gt <- ggplotGrob(g)
assign_strip_colours <- function(gt, index, colours) {
if (length(index) != length(colours))
stop()
# Decide which strips to recolour, here: the first 3
is_strips <- which(startsWith(gt$layout$name, "strip-b"))[index]
# Extract strips
strips <- gt$grobs[is_strips]
# Loop over strips
strips <- mapply(function(strip, colour) {
# Find actual strip
is_strip <- strip$layout$name == "strip"
grob <- strip$grobs[is_strip][[1]]
# Find rectangle
is_rect <- which(vapply(grob$children, inherits, logical(1), "rect"))
# Change colour
grob$children[[is_rect]]$gp$fill <- colour
# Put back into strip
strip$grobs[is_strip][[1]] <- grob
return(strip)
}, strip = strips, colour = colours)
# Put strips back into gtable
gt$grobs[is_strips] <- strips
return(gt)
}
gt <- assign_strip_colours(gt, 1:15, rainbow(15))
# Plot gtable
grid::grid.newpage(); grid::grid.draw(gt)
So I hope @teunbrand could help me. vary thankful.
In the new version, it should be easier to create varying fills for the facet strips. The facet functions have a strip argument, where you can give a strip_*(). For strip_themed() and strip_nested() you can vary the background fills.
library(ggplot2)
library(ggh4x)
# data<-structure(...) # omitted for brevity
ggplot(data = data, aes(Name,mean, label = Name,fill=Organ)) +
geom_bar(position="dodge2", stat="identity",width = 0.85,color="black") +
geom_errorbar(aes(ymin = mean - sd, ymax = mean + sd),position = position_dodge(0.85), width = .2) +
facet_nested(
.~Organ+Disease, scales="free",switch = "x",nest_line = TRUE,
strip = strip_nested(
background_x = elem_list_rect(fill = rainbow(15))
))+
theme_classic() +
theme(
plot.title = element_text(hjust = 0.5),
plot.margin = unit(c(5, 10, 10, 10), "mm"),
strip.background = element_rect(colour="black", fill="white"),
strip.text.x = element_text(size = 6, angle=0),
strip.placement = "outside")
