i have 2 datasets that span full genomes, separated by chromosomes (scaffolds), for 2 group comparisons and i want to overlap them in a single graph.
the way i was doing was as follow:
ggplot(NULL, aes(color = as_factor(scaffold))) +
geom_smooth(data = windowStats_SBvsOC, aes(x = mid2, y = Fst_group1_group5), se=F) +
geom_smooth(data = windowStats_SCLvsSCU, aes(x = mid2, y = Fst_group3_group4), se=F) +
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 (smoothed means)") +
theme_minimal() +
theme(
legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_text(),
axis.text.x = element_text(angle = 60, size = 8, vjust = 0.5))
this way, i get each chromosome with alternating colors, and the smoothing is per chromosome. but i wanted the colors to be different between the 2 groups so i can distinguish when they are overlapped like this. is there a way to do it? i can only do it once i remove the color by scaffold, but then the smoothing gets done across the whole genome and i don't want that!
my dataset is big, so i'm attaching it here!
i'm running this in rstudio 2022.02.3, R v.3.6.2 and package ggplot2
EDIT: i've figured out! i just needed to change color = as_factor(scaffold) to group = as_factor(scaffold); and then add the aes(color) to each geom_smooth() function.
I would like to plot a sophisticated graph in Julia. The code below is in Julia's version using ggplot.
using CairoMakie, DataFrames, Effects, GLM, StatsModels, StableRNGs, RCall
#rlibrary ggplot2
rng = StableRNG(42)
growthdata = DataFrame(; age=[13:20; 13:20],
sex=repeat(["male", "female"], inner=8),
weight=[range(100, 155; length=8); range(100, 125; length=8)] .+ randn(rng, 16))
mod_uncentered = lm(#formula(weight ~ 1 + sex * age), growthdata)
refgrid = copy(growthdata)
filter!(refgrid) do row
return mod(row.age, 2) == (row.sex == "male")
end
effects!(refgrid, mod_uncentered)
refgrid[!, :lower] = #. refgrid.weight - 1.96 * refgrid.err
refgrid[!, :upper] = #. refgrid.weight + 1.96 * refgrid.err
df= refgrid
ggplot(df, aes(x=:age, y=:weight, group = :sex, shape= :sex, linetype=:sex)) +
geom_point(position=position_dodge(width=0.15)) +
geom_ribbon(aes(ymin=:lower, ymax=:upper), fill="gray", alpha=0.5)+
geom_line(position=position_dodge(width=0.15)) +
ylab("Weight")+ xlab("Age")+
theme_classic()
However, I would like to modify this graph a bit more. For example, I would like to change the scale of the y axis, the colors of the ribbon, add some error bars, and also change the text size of the legend and so on. Since I am new to Julia, I am not succeding in finding the equivalent language code for these modifications. Could someone help me translate this R code below of ggplot into Julia's language?
t1= filter(df, sex=="male") %>% slice_max(df$weight)
ggplot(df, aes(age, weight, group = sex, shape= sex, linetype=sex,fill=sex, colour=sex)) +
geom_line(position=position_dodge(width=0.15)) +
geom_point(position=position_dodge(width=0.15)) +
geom_errorbar(aes(ymin = lower, ymax = upper),width = 0.1,
linetype = "solid",position=position_dodge(width=0.15))+
geom_ribbon(aes(ymin = lower, ymax = upper, fill = sex, colour = sex), alpha = 0.2) +
geom_text(data = t1, aes(age, weight, label = round(weight, 1)), hjust = -0.25, size=7,show_guide = FALSE) +
scale_y_continuous(limits = c(70, 150), breaks = seq(80, 140, by = 20))+
theme_classic()+
scale_colour_manual(values = c("orange", "blue")) +
guides(color = guide_legend(override.aes = list(linetype = c('dotted', 'dashed'))),
linetype = "none")+
xlab("Age")+ ylab("Average marginal effects") + ggtitle("Title") +
theme(
axis.title.y = element_text(color="Black", size=28, face="bold", hjust = 0.9),
axis.text.y = element_text(face="bold", color="black", size=16),
plot.title = element_text(hjust = 0.5, color="Black", size=28, face="bold"),
legend.title = element_text(color = "Black", size = 13),
legend.text = element_text(color = "Black", size = 16),
legend.position="bottom",
axis.text.x = element_text(face="bold", color="black", size=11),
strip.text = element_text(face= "bold", size=15)
)
As I commented before, you can use R-strings to run R code. To be clear, this isn't like your post's approach where you piece together many Julia objects that wrap many R objects, this is RCall converting a Julia Dataframe to an R dataframe then running your R code.
Running an R script may not seem very Julian, but code reuse is very Julian. Besides, you're still using an R library and active R session either way, and there might even be a slight performance benefit from reducing how often you make wrapper objects and switch between Julia and R.
## import libraries for Julia and R; still good to do at top
using CairoMakie, DataFrames, Effects, GLM, StatsModels, StableRNGs, RCall
R"""
library(ggplot2)
library(dplyr)
"""
## your Julia code without the #rlibrary or ggplot lines
rng = StableRNG(42)
growthdata = DataFrame(; age=[13:20; 13:20],
sex=repeat(["male", "female"], inner=8),
weight=[range(100, 155; length=8); range(100, 125; length=8)] .+ randn(rng, 16))
mod_uncentered = lm(#formula(weight ~ 1 + sex * age), growthdata)
refgrid = copy(growthdata)
filter!(refgrid) do row
return mod(row.age, 2) == (row.sex == "male")
end
effects!(refgrid, mod_uncentered)
refgrid[!, :lower] = #. refgrid.weight - 1.96 * refgrid.err
refgrid[!, :upper] = #. refgrid.weight + 1.96 * refgrid.err
df= refgrid
## convert Julia's df and run your R code in R-string
## - note that $df is interpolation of Julia's df into R-string,
## not R's $ operator like in rdf$weight
## - call the R dataframe rdf because df is already an R function
R"""
rdf <- $df
t1= filter(rdf, sex=="male") %>% slice_max(rdf$weight)
ggplot(rdf, aes(age, weight, group = sex, shape= sex, linetype=sex,fill=sex, colour=sex)) +
geom_line(position=position_dodge(width=0.15)) +
geom_point(position=position_dodge(width=0.15)) +
geom_errorbar(aes(ymin = lower, ymax = upper),width = 0.1,
linetype = "solid",position=position_dodge(width=0.15))+
geom_ribbon(aes(ymin = lower, ymax = upper, fill = sex, colour = sex), alpha = 0.2) +
geom_text(data = t1, aes(age, weight, label = round(weight, 1)), hjust = -0.25, size=7,show_guide = FALSE) +
scale_y_continuous(limits = c(70, 150), breaks = seq(80, 140, by = 20))+
theme_classic()+
scale_colour_manual(values = c("orange", "blue")) +
guides(color = guide_legend(override.aes = list(linetype = c('dotted', 'dashed'))),
linetype = "none")+
xlab("Age")+ ylab("Average marginal effects") + ggtitle("Title") +
theme(
axis.title.y = element_text(color="Black", size=28, face="bold", hjust = 0.9),
axis.text.y = element_text(face="bold", color="black", size=16),
plot.title = element_text(hjust = 0.5, color="Black", size=28, face="bold"),
legend.title = element_text(color = "Black", size = 13),
legend.text = element_text(color = "Black", size = 16),
legend.position="bottom",
axis.text.x = element_text(face="bold", color="black", size=11),
strip.text = element_text(face= "bold", size=15)
)
"""
The result is the same as your post's R code:
I used Vega-Lite (https://github.com/queryverse/VegaLite.jl) which is also grounded in the "Grammar of Graphics", and LinearRegression (https://github.com/ericqu/LinearRegression.jl) which provides similar features as GLM, although I think it is possible to get comparable results with the other plotting and linear regression packages. Nevertheless, I hope that this gives you a starting point.
using LinearRegression: Distributions, DataFrames, CategoricalArrays
using DataFrames, StatsModels, LinearRegression
using VegaLite
growthdata = DataFrame(; age=[13:20; 13:20],
sex=categorical(repeat(["male", "female"], inner=8), compress=true),
weight=[range(100, 155; length=8); range(100, 125; length=8)] .+ randn(16))
lm = regress(#formula(weight ~ 1 + sex * age), growthdata)
results = predict_in_sample(lm, growthdata, req_stats="all")
fp = select(results, [:age, :weight, :sex, :uclp, :lclp, :predicted]) |> #vlplot() +
#vlplot(
mark = :errorband, color = :sex,
y = { field = :uclp, type = :quantitative, title="Average marginal effects"},
y2 = { field = :lclp, type = :quantitative },
x = {:age, type = :quantitative} ) +
#vlplot(
mark = :line, color = :sex,
x = {:age, type = :quantitative},
y = {:predicted, type = :quantitative}) +
#vlplot(
:point, color=:sex ,
x = {:age, type = :quantitative, axis = {grid = false}, scale = {zero = false}},
y = {:weight, type = :quantitative, axis = {grid = false}, scale = {zero = false}},
title = "Title", width = 400 , height = 400
)
which gives:
You can change the style of the elements by changing the "config" as indicated here (https://www.queryverse.org/VegaLite.jl/stable/gettingstarted/tutorial/#Config-1).
As the Julia Vega-Lite is a wrapper to Vega-Lite additional documentation can be found on the Vega-lite website (https://vega.github.io/vega-lite/)
I created my own theme and now I also want to standardize the color set that is used. I tried to do this with the list solution, provided in the answer of Viktor in this feed:
Associate a color palette with ggplot2 theme
df <- mtcars
uwvPalet <- c("#0078D2","#003282","#C4D600")
theme_uwv <- function(base_size = 22, base_family = "Verdana"){theme_hc(base_size = base_size, base_family = base_family)%+replace%theme(plot.title = element_text(color = rgb(0, 120, 210)), complete = TRUE)}
theme_uwv2 <- list(theme_uwv, scale_color_manual(values = uwvPalet))
ggplot(df, aes(fill = cyl, x = am, y = mpg)) + geom_bar(position = "dodge", stat="identity") + theme_uwv2()
Unfortunately, I get the error:
Error in theme_uwv2() : could not find function "theme_uwv2"
Anyone know how I can fix this?
The following worked for me. theme_uwv2 needed the value returned from theme_uwv() as a list element, not the function itself. Also, you were making a plot where the fill was the dominant colour variable, so I've substituted scale_color_manual() with scale_fill_manual() for demonstration purposes.
library(ggplot2)
library(ggthemes)
df <- mtcars
uwvPalet <- c("#0078D2","#003282","#C4D600")
theme_uwv <- function(base_size = 22, base_family = "Verdana"){
theme_hc(base_size = base_size, base_family = base_family) %+replace%
theme(plot.title = element_text(color = rgb(0, 120, 210, maxColorValue = 255)),
complete = TRUE)}
theme_uwv2 <- list(theme_uwv(), scale_fill_manual(values = uwvPalet))
ggplot(df, aes(fill = as.factor(cyl), x = am, y = mpg)) +
geom_col(position = "dodge") +
ggtitle("test") +
theme_uwv2
I am trying to plot how different predictors associate with stroke and underlying phenotypes (i.e. cholesterol). In my data, I originally had working ggplot code in which shapes denoted the different variables (stroke, HDL cholesterol and total cholesterol) and colour denoted type (i.e. disease (stroke) or phenotype (HDL/total cholesterol). To make it more intuitive, I want to swap shape and colour around but now that I do this, I am having issues with position dodge and the alignment of geom_point and geom_error
stroke_graph <- ggplot(stroke,aes(y=as.numeric(stroke$test),
x=Clock,
shape = Type,
colour = Variable)) +
geom_point(data=stroke, aes(shape=Type, colour=Variable), show.legend=TRUE,
position=position_dodge(width=0.5), size = 3) +
geom_errorbar(aes(ymin = as.numeric(stroke$LCI), ymax= as.numeric(stroke$UCI)),
position = position_dodge(0.5), width = 0.05,
colour ="black")+
ylab("standardised beta/log odds")+ xlab ("")+
geom_hline(yintercept = 0, linetype = "dotted")+
theme(axis.text.x = element_text(size = 10, vjust = 0.5), legend.position = "none",
plot.title = element_text(size = 12))+
scale_y_continuous(limit = c(-0.402, 0.7))+ scale_shape_manual(values=c(15, 17, 18))+
theme(legend.position="right") + labs(shape = "Variable") + guides(shape = guide_legend(reverse=TRUE)) +
coord_flip()
stroke_graph + ggtitle("Stroke and Associated Phenotypes") + theme(plot.title = element_text(hjust = 0.5))
Graph now: 1
Previously working graph - only difference in code is swapping "Type" and "Variable": 2