I have this plot, but i want to change around the order of the X axis labels.
It should start with the site number (eg. X27a, X28a, W15c, W17c) Then the group (eg. A, B, C, D) and then the last one.
So basically i want the very bottom row of labels at the top.
How do i reorder it?
Code
ggplot(data = inf, aes(x = COMPARTMENT, y = MI, fill = SPECIES)) +
geom_bar(stat = "identity") +
scale_y_continuous(expand = c(0, 0), limits = c(-0.1, 12.5), breaks = 2*c(0:6)) +
theme_bw() +
facet_grid(~COMP.COMP*REGION, switch = "x", scales = "free_x", space = "free_x") +
theme(strip.text.x = element_text(size = 10)) +
theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5, size = 10)) +
theme(panel.spacing = unit(0, "lines"),
strip.background = element_blank()) +
scale_fill_manual(name = "SPECIES",
values=c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2")) +
ylab("Average infestation rate (%)") +
xlab("Compartment by Comparable Groups by Region") +
theme(panel.grid.major.y = element_line("lightgray"),
panel.grid.major.x = element_blank()) +
theme(axis.line = element_line(color = "black"),
legend.position = "right",
legend.title=element_text())
Related
I have a genome-wide dataset that I'm trying to plot in the following way:
Have each chromosome be a separate color
Have specific windows highlighted by a bar (I'm using geom_vline) - this I'm getting from a
separate table
Have only geom_vline feature in the legend
I have tried many different things, but it seems I cannot have all three together!
Here is the link to both datasets:
allStats & allStats_fstPi_group15
With this code, I can have the first 2, but not the 3rd:
ggplot(allStats, aes(x = mid2, y = Fst_group1_group5,
color = as_factor(scaffold))) +
geom_point(size = 2) +
geom_vline(xintercept = chrom$add, color = "grey") +
scale_y_continuous(expand = c(0,0), limits = c(0, 1)) +
scale_x_continuous(labels = chrom$chrID, breaks = axis_set$center) +
scale_color_manual(values = rep(c("#276FBF", "#183059"), unique(length(chrom$chrID)))) +
scale_size_continuous(range = c(0.5,3)) +
labs(x = NULL,
y = "Fst SBM vs OC") +
theme_minimal() +
theme(
legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
panel.grid.major.y = element_blank(),
panel.grid.minor.y = element_blank(),
axis.title.y = element_text(),
axis.text.x = element_text()) +
geom_vline(data = allStats_fstPi_group15,
aes(xintercept = allStats_fstPi_group15$mid2),
color = "orange", show.legend = T)
With this one I can get 2 and 3 only (I'm not able to color code each block separately):
cols <- c("SBM vs OC" = rep(c("#276FBF", "#183059"), unique(length(chrom$chrID))),
"90th percentile (Fst vs Pi)" = "orange")
ggplot(allStats, aes(x = mid2)) +
geom_point(aes(y = Fst_group1_group5,
color = as_factor(scaffold)),
size = 2) +
geom_vline(data = allStats_fstPi_group15,
aes(xintercept = allStats_fstPi_group15$mid2,
color = "90th percentile (Fst vs Pi)")) +
scale_color_manual(values = cols)
I've seen the issue with the legend being that color needs to be within aes(), so my question is: is it impossible what I'm trying to do?
I have a plot like this:
library(ggplot2)
library(reshape2)
library(ggh4x)
data <- data.frame(col1=c("Sample1","Sample2","Sample3","Sample4","Sample5","Sample6"),
col2=c(0.5,0.1,0.4,0.05,0.05,0.9),
col3=c(0.6,0.1,0.3,0.1,0.1,0.8),
col4=c(0.5,0.3,0.2,0.05,0.15,0.8),
col5=c("a","a","a","b","b","b"),
col6=c("c","c","c","c","c","c"))
data2 <- melt(data)
ggplot(data=data2, aes(x = variable, y = value, fill=col1))+
geom_bar(position="stack", stat="identity")+
scale_fill_manual(values=c("#e6194B","#ffe119","#f58231","#911eb4","#42d4f4","#bfef45")) +
scale_y_continuous(expand = c(0, 0),labels = scales::percent) +
facet_nested(~col6 + ~col5, scales = "free_x",space = "free_x",switch = "x") +
ggtitle("Title") +
theme_classic() +
theme(strip.text.y = element_text(angle=0),legend.position = "right",
legend.key.size = unit(0.4, 'cm'),
axis.line = element_line(colour = "black"),
axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1),
strip.placement = "outside",
strip.background = element_rect(color = "white", fill = "white"),
axis.title = element_blank()) +
guides(fill=guide_legend(title=NULL, ncol = 1)) +
xlab("X axis") +
ylab("Y axis")
Which creates a barplot like this:
Please take a look
My question is simple, how can I set y-axis starting value to 10% instead of 0% (without changing the code too much). All answers are greatly appreciated! (Similar questions are checked, without success...)
While in general not recommended for bar charts one option to "set" the starting point would be to set the limits via coord_cartesian:
library(ggplot2)
library(ggh4x)
ggplot(data = data2, aes(x = variable, y = value, fill = col1)) +
geom_bar(position = "stack", stat = "identity") +
scale_fill_manual(values = c("#e6194B", "#ffe119", "#f58231", "#911eb4", "#42d4f4", "#bfef45")) +
scale_y_continuous(expand = c(0, 0), labels = scales::percent) +
facet_nested(~ col6 + ~col5, scales = "free_x", space = "free_x", switch = "x") +
ggtitle("Title") +
theme_classic() +
theme(
strip.text.y = element_text(angle = 0), legend.position = "right",
legend.key.size = unit(0.4, "cm"),
axis.line = element_line(colour = "black"),
axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1),
strip.placement = "outside",
strip.background = element_rect(color = "white", fill = "white"),
axis.title = element_blank()
) +
guides(fill = guide_legend(title = NULL, ncol = 1)) +
xlab("X axis") +
ylab("Y axis") +
coord_cartesian(ylim = c(.1, NA))
I made to build this chart with ggalluvial but I couldn't manage to put the labels in a proper way that is not overlapping. Does anyone know what I can do to make it better? I was thinking in make the space between the bars wider but I didn't manage to do it.
So far I did this:
ggplot(data = alluvialTransposedNA,
aes(x = x, stratum = stratum, alluvium = id,
y = Freq, fill = Agency, label = stratum)) +
scale_x_discrete(expand = c(.1, .1)) +
scale_y_continuous(expand = c(.2, .2)) +
geom_alluvium(aes(fill = Agency), width = 1/6) +
geom_stratum(width = 1/3, alpha = 1.5) + +
geom_label(stat = "stratum", aes(label = after_stat(stratum)),size=2) +
theme(legend.position = "bottom",
axis.text.x = element_text(angle = 45, vjust = 0.75, hjust=1),
axis.title.x = element_blank(),
axis.title.y = element_blank(),
axis.ticks = element_blank(),
plot.title = element_text(hjust = 0.5)) +
guides(fill=guide_legend(override.aes = list(color=mycolors[1:2])))+
ggtitle("Evolution topics during covid-19")
I would like to know if it's possible to modify the ticks of x axis with a ggplot pie chart.
Here what I can do :
# Some colors
couleurs <- data.frame(
id=seq(1,17,1),
mix=c(c(rep(1,6),rep(2,7),rep(3,4))),
html=c("#A00020","#109618","#388EE4","#C484D1","#FFAA33","#CCCDD0","#004AC5","#F80094","#CB5023","#638995","#33CFCF","#95DC4E","#F7D633","#5C403C","#F72020","#00D96C","#FDE4C5")
)
couleurs$html <- factor(couleurs$html, levels = couleurs$html[order(couleurs$id, decreasing = FALSE)])
# Data
activite <- data.frame(label=c("B to B","B to C","B to B / B to C", "B to B"), cible=c(rep("Externe",3), "Interne"), nb=c(12,9,3,12))
activite$label <- factor(activite$label, levels = activite$label[order(activite$nb[activite$cible=="Externe"], decreasing = TRUE)])
library(plyr)
activite<-ddply(activite,.(cible),transform,pc=(nb/sum(nb))*100)
activite
# Pie chart
library(ggplot2)
ggplot(data = activite, aes(x = "", y = nb, fill = label )) +
geom_bar(stat = "identity", position = position_fill(), width = 1) +
coord_polar(theta= "y", start = 0, direction = -1) +
labs(fill="") +
scale_fill_manual(values=as.character(couleurs$html[1:nrow(activite)]), labels=paste(activite$label,"\t\t\t",sep="")) +
geom_text(aes(label = paste(pc,"%", sep=" ")), size=4, colour = "white", fontface = "bold", position = position_fill(vjust = 0.5)) +
theme(strip.text = element_text(size=20, face = "bold", ), strip.background = element_rect(fill="grey75")) +
theme(panel.background = element_rect(fill = "white")) +
theme(plot.background = element_rect(fill = "grey92")) +
theme(legend.position="bottom", legend.background = element_rect(fill="grey92")) +
theme(legend.key = element_blank()) +
theme(panel.grid.minor = element_blank(), panel.grid.major = element_line(colour = "grey75")) +
theme(axis.text.y = element_blank()) +
theme(axis.ticks.length = unit(0, "mm")) +
theme(axis.title.x = element_blank(),axis.title.y = element_blank()) +
theme(legend.box.spacing = unit(1, "mm")) +
facet_wrap(~ cible)
Here my result:
After several hours of serach, I didn't find a solution to create what I want. The exact same pie chart but with personalised ticks like that :
With these particular conditions :
- do not change the direction of the data in the pie chart, I want it like exactly this
- if possible (but if not possible, it's okay), I would like the ticks' labels not superposed with the axis.
If someone can help me, I would really appreciate.
Here's one solution:
ggplot(data = activite %>%
group_by(cible) %>%
arrange(desc(nb)) %>%
mutate(axis.label = cumsum(nb),
axis.position = cumsum(pc)/100) %>%
mutate(axis.label = ifelse(pc == min(pc),
paste(axis.label, "0", sep = "-"),
axis.label)),
aes(x = 1, y = nb, fill = label )) +
geom_segment(aes(x = 1, xend = 1.6, y = axis.position, yend = axis.position),
colour = "grey75") +
geom_vline(xintercept = 1.6, colour = "grey75") +
geom_bar(stat = "identity", position = position_fill(reverse = T), width = 1) +
coord_polar(theta= "y", start = 0, direction = 1) +
labs(fill="") +
scale_fill_manual(values=as.character(couleurs$html[1:nrow(activite)]), labels=paste(activite$label,"\t\t\t",sep="")) +
geom_text(aes(label = paste(pc,"%", sep=" ")), size=4, colour = "white",
fontface = "bold", position = position_fill(vjust = 0.5, reverse = T)) +
geom_text(aes(x = 1.7, label = axis.label), size = 3,
position = position_fill(reverse = T)) +
theme(strip.text = element_text(size=20, face = "bold", ), strip.background = element_rect(fill="grey75")) +
theme(panel.background = element_rect(fill = "white")) +
theme(plot.background = element_rect(fill = "grey92")) +
theme(legend.position="bottom", legend.background = element_rect(fill="grey92")) +
theme(legend.key = element_blank()) +
theme(panel.grid = element_blank()) +
theme(axis.text = element_blank()) +
theme(axis.ticks = element_blank()) +
theme(axis.title = element_blank()) +
theme(legend.box.spacing = unit(1, "mm")) +
facet_wrap(~ cible)
Explanation:
The sequence in your labels went clockwise, while the direction of the polar coordinates went counter-clockwise. That makes labelling rather troublesome. I switched the direction for polar coordinates, & added reverse = T inside the position adjustment calls for the geoms.
It's hard to assign different axis breaks to different facets of the same plot, so I didn't. Instead, I modified the data to include calculated axis labels / margin positions, added margins via geom_segment / geom_vline, & hid the axis text / ticks in theme().
I made horizontal barplot. I need to move x-axis up, so it is placed not under the last bar, but under some bar, picked based on other criterion.
I've tried some things, like gtable, but with no success. I would appreciate any help.
This is a picture that illustrats what I want to achieve:
Here is the code to produce sample horizontal barplot:
library("ggplot2")
library("RColorBrewer")
colours <- brewer.pal(11, "RdYlGn")[3:9]
no.names <- 4
name.percentage <- data.frame(name = paste0(LETTERS[1:no.names], letters[1:no.names], sample(LETTERS[1:no.names], size = no.names, replace = TRUE )), percentage = 0.85 + runif(no.names, 0, 0.15))
name.percentage <- rbind(
transform(name.percentage, type = 1, fill = cut(percentage, breaks = c(-Inf,(1:6 * 3 + 81)/100, Inf), right = T, labels = colours)),
transform(name.percentage, percentage = 1 - percentage, type = 2, fill = "#EEEEEE")
)
plot <- ggplot(data = name.percentage,
aes( x = name, y = percentage, fill = fill)) +
geom_bar(stat = "identity", position = "stack", width = 0.75) +
scale_fill_identity(guide = "none") +
labs(x = NULL, y = NULL) +
scale_y_continuous(expand = c(0,0)) +
scale_x_discrete(expand = c(0,0)) +
coord_flip() +
theme_classic() +
theme(axis.ticks.y = element_blank(),
axis.text.y = element_text(size = 11, colour = "black" ),
axis.text.x = element_text(size = 11, colour = "black" ),
axis.line = element_blank(),
plot.margin = grid::unit(c(5,5,5,5),"mm"),
aspect.ratio = ((no.names %% 30) / 30 ) * 1.70)
print(plot)
You could create two separate plots first, removing the axis ticks and labels in one of them entirely:
plot1 <- ggplot(data = subset(name.percentage, name=="AaC" | name=="BbA"),
aes( x = name, y = percentage, fill = fill)) +
geom_bar(stat = "identity", position = "stack", width = 0.75) +
scale_fill_identity(guide = "none") +
labs(x = NULL, y = NULL) +
scale_y_continuous(expand = c(0,0)) +
scale_x_discrete(expand = c(0,0)) +
coord_flip() +
theme_classic() +
theme(axis.ticks.y = element_blank(),
axis.text.y = element_text(size = 11, colour = "black" ),
axis.text.x = element_blank(),
axis.line=element_blank(),
axis.ticks=element_blank(),
axis.title.x=element_blank(),
axis.title.y=element_blank(),
aspect.ratio = ((no.names %% 30) / 30 ) * 1.70)
plot2 <- ggplot(data = subset(name.percentage, name=="CcA" | name=="DdD"),
aes( x = name, y = percentage, fill = fill)) +
geom_bar(stat = "identity", position = "stack", width = 0.75) +
scale_fill_identity(guide = "none") +
labs(x = NULL, y = NULL) +
scale_y_continuous(expand = c(0,0)) +
scale_x_discrete(expand = c(0,0)) +
coord_flip() +
theme_classic() +
theme(axis.ticks.y = element_blank(),
axis.text.y = element_text(size = 11, colour = "black" ),
axis.text.x = element_text(size = 11, colour = "black" ),
axis.line = element_blank(),
aspect.ratio = ((no.names %% 30) / 30 ) * 1.70)
Then you can use plot_grid from package cowplot to arrange the two plots, with align="h" aligning both plots horizontally:
library(cowplot)
plot_grid(plot2, plot1, align="h", ncol=1)