Tag: ggplot2

Plot Titles, Axes and Legend Titles. One way to modify plot titles, axes and legend titles is through the labs() function in ggplot2.In order to add math notation to those labels, we can use the expression() function to specify the label text. For example, if we wanted to modify the…

The @benson23 answer is correct, if you want more control you can use manual scales for different aesthetics. If you use linetype in aes instead of fill, you will get a legend as above, if you like that more. library(tidyverse) df <- tribble( ~ tree, ~ o18, “A”, 15, “A”,…

DOI: 10.18129/B9.bioc.genomation     Summary, annotation and visualization of genomic data Bioconductor version: Release (3.6) A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome…

Box Plots Using plotly library(plotly) # data sample data <- c(1, 2, 2, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5, 5) plot_ly(y = data, type = “box”) This code creates a box plot of the data provided in the data variable. You can further customize the…

[This article was first published on coding-the-past, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here) Want to share your content on R-bloggers? click here if you have a blog, or here if you don’t. 1. What is a violin plot? A violin…

DOI: 10.18129/B9.bioc.BioNERO     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see BioNERO. Biological Network Reconstruction Omnibus Bioconductor version: 3.15 BioNERO aims to integrate all aspects of biological network inference in a single package, including data preprocessing, exploratory analyses, network inference, and analyses…

Adonis2 inR 0 When I plot my data set in ggplot, I get next to no separation of groups, yet when I run it with Adonis2, I get a p<0.05. What am I doing wrong? I did it before some time ago with a different data set. The difference now…

Is there a way to have this plot squeezed a little so labels of extreme cases (A and G) have could show up completely. code: x <- LETTERS[1:11] y <- c(9, 4, 6, 8, 5, 7, -9, -4, -6, -8, -5) z <- seq(-1, 1, by = 0.2) dat <-…

Hamblin MT, Di Rienzo A. Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus. Am J Hum Genet. 2000;66:1669–79. Article  CAS  PubMed  PubMed Central  Google Scholar  Hamblin MT, Thompson EE, Di Rienzo A. Complex signatures of natural selection at the Duffy blood group…

There’s a couple of ways to do this. You could simply log manually and inverse transform the labels in scale_y_continuous rnorm(64) %>% tibble(kbps = .) %>% ggplot() + stat_ecdf(aes(x = kbps, y = log10(1 – after_stat(y))), pad = FALSE) + scale_y_continuous(‘1 – cdf (log scale)’, breaks = seq(-3, 0), labels…

I am looking for help with code for adding clustered standard errors to a two-way bar chart generated using ggplot. All of the packages I find are for regression results. I have data in which 1200 respondents each rated 10 profiles (n=12,000). I want to plot the means (Y) by…

The specific environmental/history/collection context The Huseby Klev materials were unearthed and collected by archaeologists (including two of the co-authors of this article) during the excavation of this coastal hunter-fisher-gatherer site in the 90s50. The material assemblage was rich and well preserved: human bones, animal bones, plant remains and pieces of…

Animals and samples The study included 10 pigs, 8 pigs were bred at the INRAE experimental farm (doi.org/doi.org/10.15454/1.5572415481185847E12) and 2 pigs come from breeding organizations in accordance with the French and European legislation on animal welfare. The animals belong to the same family, except for one LW animal. Animals were…

Forgive me if this post is messy, I’m new to this! I’m analyzing RNA Seq data and found that one of my samples is an outlier (sample AV17). I’m trying to exclude it from my analysis, but whenever I do, using this code: dds = subset(countData, select = -c(AV17) ),…

While we don’t have your data, the issue is that you map a factor or character (aka SmokeType) on the y aesthetic, which when used with geom_col gives weird charts and axes scales which is evident from both of your plots. From your charts and code you want a barchart…

Hi, I am very new to R-Studio but a few months I had taken an 8-week course in which I was taught to use R-Studio for academic purposes. I recently decided to review some of the exercises we were provided with. However, I have now started to have trouble loading…

I pulled some data from Fama French web site on operating data by month…here is my code that works (below). I have 7 columns of data, with headers, including Date. I have successfully graphed one column data, but I would like to add several of the other columns of data…

I’m desperately trying to add inventory data (available online, as in this reproducible example below) in ggplot with a background of France, so that I can visualize the areas where there are no records of my species. However, I want to do it with hexagons and not points. So, I…

ConciseR data.table helper is an expert GPT model focused on providing concise answers and explanations for R programming, data.table, and ggplot2. The model is tailored to assist users with merging data.tables, plotting time series data, optimizing data.table operations, creating multi-panel plots, running functions across multiple variables, creating multiple variables, and…

This question already has answers here: Closed 12 hours ago. I am fairly new to R and working on a practice case study to sharpen my skills. I’m running into issues with the line chart visualization for this data. I need to display monthly data, but I would like to…

Join us for a 3-part workshop series meant to introduce you to R and RStudio. We will walk through the basics of how to handle data in R and how you can create data visualizations! Please note: There is one meetup link per workshop, please register for each workshop separately….

I am pretty new to R/working with data and am trying to change the title of the legend in a visualization I made. I have tried using fill= in the labels() function I have but it adds another legend for some reason. I have looked around for a solution and…

I want to make a stack bargraph, but I don’t want the same group values to sum, I just want them to stack. For example, if I have this dataset: data <- data.frame( col1 = c(“A”, “A”, “B”, “B”, “B”, “C”, “D”, “D”, “D”), col2 = c(5, 7, 1, 5,…

As a very late contribution to TidyTuesday challenge of Bob Ross’s Paintings, I have tried to plot 10 paintings of Bob Ross. Without further background, here is my code; library(tidyverse) library(showtext) library(showtextdb) library(ggthemes) library(ggtext) library(magick) library(ggimage) library(cropcircles) library(cowplot) library(patchwork) font_add_google(“Lora”, bold.wt = 700, family = “plottitle”) font_add_google(“Roboto Slab”, family =…

You have both the fill and the pattern aesthetic mapped to the same variable, so you can combine the legends simply by giving these aesthetics the same names. You didn’t include kata_difilter or ftj in your question, so the plot is not fully reproducible, but I have recreated a modified…

Hello, I don’t know how to overlay a histogram with a frequency polygon in the same graphic using ggplot2, it’s for a work and I can only use ggplot2.This is my code with the definition of the histogram and the frequency polygon library(ggplot2)library(readxl) data <- countries_of_the_world #Histogramqplot(x = data$Deathrate,geom =…

R version 4.3.1 library(ggplot2) version 3.4.2 I want to use ggplot2 bar charts to display the percentage frequency of a particular concentration class. I have five concentration classes (=c1 with the options “1_”, “2_”, “3_”, “4_”, “5_”) for which an event can occur “Early” (=c2 dichotomous with “yes” or “no”)…

I am trying to plot some data relating to carbon storage using ggplot2 in R. I am able to plot each data feature against the target variable ‘carbon’, but when I do so there are so many ticks on the x axis that the numbers become illegible. The issue lies…

This code makes a bar plot that displays the proportion of fish with ingested microplastics across several 5-year bins. I also want it to display the proportion of each species by stacking different colors. My problem with the plot produced with this code is that it adds up the proportions…

I would like to put some additional information, e.g. numbers and fractions, into a panel legend for my plots, and I would like to provide the count of rows where a value is >= some threshold. My legend is made using sprintf(“N=%d fn=%.3f …”,var1,var2,…). How can I put a “>=”…

This question was caused by a typo or a problem that can no longer be reproduced. While similar questions may be on-topic here, this one was resolved in a way less likely to help future readers. I am trying to annotate a ggplot point and line graph. It works in…

Say we have this dataframe: one<- rep(c(“a”,”b”,”c”),each=5) two <-(1:15) three<-c(1,2,3,4, 2,4,6,8,10,12,14, 3,6,9,12) df<-data.frame(one,two,three) and we create a scatter plot: ggplot(df, aes(x=two, y=three)) + geom_point() And say we suspect that there is some hidden information in the scatterplot that would become clear if we overlay three regression lines on the scatter…

* gnu/packages/bioinformatics.scm (r-sccustomize): Update to (git-version 2.0.1 revision commit). Change-Id: I4e4b499a658eaed0396263d1d9fd277a541a13d9 — gnu/packages/bioinformatics.scm | 87 ++++++++++++++++—————– 1 file changed, 43 insertions(+), 44 deletions(-) Toggle diff (108 lines) diff –git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2546454acd..3e7b99ee61 100644 — a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10245,55 +10245,54 @@ (define-public r-presto (license license:gpl3)))) (define-public r-sccustomize – (let…

I would leave room for extending your package here by getting scale_color_ipea to create an S3 class object, and then define a ggplot_add method. This mechanism allows you to interrogate the plot object to fully automate the selection of discrete or continuous scales based on the data type. scale_color_ipea <-…

I am trying to plot a time series, and notice that the date_time label for the x-axis is not formatting as expected. library(ggplot2) My_df = data.frame(My_datetime = seq(from = as.POSIXct(“2019-05-21 8:00:00”), to = as.POSIXct(“2019-05-22 23:00:00”), by = “10 min”), My_data = sin(1:235)) ggplot(data = My_df) + geom_line(aes(x = My_datetime, y…

Suppose your data looks something like this: set.seed(2) df <- data.frame(SBP = sample(101:199, 1000, TRUE)) df$survived <- c(‘yes’, ‘no’)[rbinom(1000, 1, (df$SBP – 100)/200) + 1] head(df) #> SBP survived #> 1 185 no #> 2 179 yes #> 3 170 no #> 4 106 yes #> 5 132 yes #>…

Is there a way to set the edge of a ggplot bar chart to a particular axis value? So, for the example below, I would like the right hand edge of the plot to be at 0.4, thus cutting off the “virginica” bar. library(ggplot2) data(“iris”) df <- as.data.frame(data(“iris”)) ggplot(data =…

Here is one option to achieve your desired result using stat_summary and a custom function to be passed to the fun.data argument. Besides computing the desired stats the function also adds some additional columns including the labels, the vertical alignment and the y label position. Additionally, besides using after_stat note…

Sure could this be achieved but I don’t know of any easy and general approach and hence at least for the approach below it requires some fiddling to position the legend and to set the height of the colorbar. Note that all these values are also dependent on the size…

Participants and blood collection A total of n = 23 HIV-1 seropositive individuals on stably suppressive ART were included in this study (Supplementary Table 1). Participants were recruited at Ghent University Hospital. 2/23 individuals are female, 21/23 are male; the limited representation of female individuals in our study is a direct reflection of…

Lung cancer ICB cohort Advanced non-small cell lung carcinoma patients who were treated with anti-PD-1/PD-L1 monotherapy at Samsung Medical Center, Seoul, Republic of Korea were enrolled for this study. The present study has been reviewed and approved by the Institutional Review Board (IRB) of the Samsung Medical Center (IRB no….

Usually, a scatterplot requires a data column for the x and one for the y column, as for example here: r-graph-gallery.com Basic scatterplot with R and ggplot2 This post provides reproducible code and explanation for the most basic scatterplot you can build with R and ggplot2. Now lets suppose I…

I have the following R code library(“ggplot2”) GDP_data <- read.csv(“US GDP.csv”, header=FALSE, sep=”,”) GDP_data = data.frame(GDP_data) names(GDP_data) <- GDP_data[1,] GDP_data <- GDP_data[-1,] plot(x=GDP_data[“level-current”], y=GDP_data[“date”], type=”l”,col=”red”, main=””) summary(GDP_data) returns these columns: date level-current level-chained change-current change-chained Length:86 Length:86 Length:86 Length:86 Length:86 Class :character Class :character Class :character Class :character Class :character…

I’m looking for a way to insert charts and tables into a Word document that already has headers and titles in place. My plan is to replace specific words within the document, such as “Graph1” and “Table1,” with the actual charts and tables. I would appreciate any suggestions on how…

I am trying to create a trend plot using a variable that represents 12 different groups which has 12 trend lines but I want to put a label at the end so that its clear which line represents which group but I get this error: ggrepel: 11655 unlabeled data points…

Hi all I am currently facing an issue while working with the microbiome package in R and would greatly appreciate your insights. > b.lgg <- divergence(subset_samples(physeq, Description == “Stool_controls”), + apply(abundances(subset_samples(physeq, Description == “Stool_controls”)), 1, median)) > b.pla <- divergence(subset_samples(physeq, Description == “Stool_samples”), + apply(abundances(subset_samples(physeq, Description == “Stool_samples”)), 1, median))…

I would like some help please with a question about facet_wrap in R Here is some example data library(tidyverse) score <- c(6,5,3,2,2,1,4,5,3,4,5,4,3,2,2,2,4,6) time <- c(1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2) set <- c(1,1,1,1,1,1,1,1,2,2,3,3,3,3,3,3,3,3) ID <- c(1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9) df <- data.frame(score, time, set, ID) plot <- ggplot(df, aes(x = time, y = score, group = ID)) +…

Problem You want to modify the legend of a graph made with ggplot2. Solution Start with an example graph with the default options: library(ggplot2) bp <- ggplot(data=PlantGrowth, aes(x=group, y=weight, fill=group)) + geom_boxplot() bp Removing the legend Use guides(fill=FALSE), replacing fill with the desired aesthetic. You can also remove all the…

One option would be to switch to ggtext::element_markdown which has a lot more options than element_text and allows to for an outline: library(ggplot2) library(ggtext) df <- as.data.frame(data(“iris”)) ggplot(data = iris, aes(x = Species, y = Petal.Width)) + geom_bar(stat = “identity”, position = “identity”) + labs(caption = “Add box around me”)…

Data science and programming have become increasingly important in today’s world, and two languages have emerged as the top contenders: R and Python. Many newcomers to the field often find themselves wondering which language is more challenging to learn and master. Let’s take a closer look at the complexities of…

Course Description This class will introduce students to data visualization using the R and ggplot2 software. Students will learn the principles underlying ggplot2, how to prepare and manipulate datasets in order to create basic visualization such as barplots, scatterplots, line plots and panelled plots. As a prerequisite, students should have…

Course Description This class will build on material in the introductory class to create more advanced visualizations such as adding text annotations, custom themes and interactivity. As a prerequisite students should have some familiarity with R and ggplot2. Instructor Bio Simon Kiss is an Associate Professor of Human Rights and…

A fierce debate has been brewing in the data science community: which programming language reigns supreme for statistical analysis? Python and R have emerged as the heavyweight contenders, each with its own dedicated following. While they share similarities in their data manipulation and visualization capabilities, the question remains: can Python…

I am attempting to produce a boxplot with the results of a significance text, ideally with Student’s test and/or a Wilcoxon’s test comparing two groups of concentrations between two different auto-analysers. If I run the following code (Note the code does not include the input statements for the datafiles but…

Cristina Ageitos, Aleix Benavente, Luna Campos, Alex Espelt, Maria Sirera R-SCRIPT #COMMANDS ON THE FINAL PROJECT: “Income disparities in public transport usage” #Its structure follows the structure of the written project #The data used for each test corresponds to the one added in the document, with the title “Data used”,…

# SCRIPT: VerticalProfilePlotter.R # # This script is designed to plot vertical profiles of parameters provided in a data file. The parameters include # Depth (m), Temperature (oC), Chlorophyll (micrograms per L), and Light (%). The script utilizes the ggplot2 package # for creating the plots. The data file should…

I made code for a boxplot in R version 3.6.1: ggplot(Data_Addi, aes(x=as.factor(Sex), y=DEFS_SF, fill=as.factor(Diagnosis_Addison_Recoded))) + geom_boxplot(outlier.shape=NA, color=”black”) + geom_jitter(position=position_jitterdodge(),show.legend = FALSE) + theme_bw(base_size = 25) + scale_x_discrete(name=””, breaks=c(“1”, “2”),labels=c(“Females”, “Males”)) + scale_fill_manual(name=”Diagnostic Group”, breaks=c(“1”, “2”), labels=c(“Addison”,”Control”), values=c(“white”, “grey”)) + labs(title=”Executive function total”, x=”Sex”, y=”BDEFS-SF Total Score”) This gave the following…

# SCRIPT: VerticalProfilePlotter.R # # This script contains a function that plots vertical profiles of parameters provided as input. # The parameters include Depth, Temperature, Chlorophyll, and Light. The function utilizes the # ggplot2 package for creating the plots. # Required Packages: # – ggplot2: A data visualization package in…

This is my R code:#loading the necessary libraries library(tidyverse) library(ggplot2) # importing the data hotel_bookings <- read.csv(“hotel_bookings.csv”) However when i run this code the notebook cannot find the dataset. The dataset is in this link:www.kaggle.com/datasets/mojtaba142/hotel-booking?select=hotel_booking.csv. how do i add this dataset so that i can run the above codes without…

Article Summary Box Efficient data preparation in RStudio hinges on automated data cleaning techniques, significantly reducing manual errors and streamlining the initial stages of analysis. Vectorized operations and the apply() family functions in RStudio dramatically enhance data manipulation efficiency, especially for large datasets. Utilizing multiple linear regression and PCA in…

Animals All experimental procedures were performed in compliance with animal protocols approved by the Institutional Animal Care and Use Committee at Boston Children’s Hospital (Protocol no. 20-05-4165 R). Mice were provided with food and water ad libitum, housed on a 12-hour light/dark schedule (7 a.m.–7 p.m. light period) with no more than five mice…

Histogram in ggplot2 1 I’m willing to do a histogram with boxplot bar in ggplot2. I already have a well functioning code for a jitter graph, which give me colors for each variable. ggplot(Raiz, aes(x = G, y = T, color = c(‘WT’, ‘at5g01950’)[2 – (as.numeric(G) %% 2)])) + geom_jitter(position…

How to put spaces between bars in ggplot2 barplot 2 Hi, I want to put spaces between each pair of bars in my barplot. This is my code ggplot(Germ, aes(x = G, y = T, color = c(‘WT’, ‘at5g01950’)[2 – (as.numeric(G) %% 2)])) + geom_bar(position=”dodge”, stat=”identity”) + geom_boxplot(width = 0.5,…

I want to make the barplot columns fillet by the red and blue, not the gray. This is my code ggplot(Germ, aes(x = G, y = T, color = c(‘WT’, ‘at5g01950’)[2 – (as.numeric(G) %% 2)])) + geom_bar(position=”dodge”, stat=”identity”) + geom_boxplot(width = 0.5, color = “black”, alpha = 0.2, position =…

Hello, I’m new using RStudio. I’m trying to show the distribution of temperature values (min,max and mean) in a graphic, my database is called ‘datos_diarios’ and I already imported the library, but it doesn’t seem to work with this code…It also shows the values on the X axis way too…

I want to make a model and plot that shows how long it takes for salmon lice to lay eggs and how the time differ between wild and farmed salmon lices. Then I want to make a table or paragraph that uses the plot. I tried to use Phind to…

Sindy Saintclair Thursday, December 16, 2021 Lesson 5 – Statistical Plots LearningObjectives and Questions Notes and Answers Installing andUsing PackagesArgumentNamesWhat is ggplot2? R has many different systems to create plots of data; the two most popular ones areR Base Graphics and a system calledggplot2.R Base Graphics is built into R;…

I’m willing to do a histogram with boxplot bar in ggplot2. I already have a well functioning code for a jitter graph, which give me colors for each variable. ggplot(Raiz, aes(x = G, y = T, color = c(‘WT’, ‘at5g01950’)[2 – (as.numeric(G) %% 2)])) + geom_jitter(position = position_jitter(width = 0.2),…

Article Summary Box Familiarize yourself with RStudio’s help system, which is essential for efficient programming. Strategies for accessing detailed documentation for specific R packages directly within RStudio. Leverage RStudio’s advanced search features for streamlining the process of finding relevant help information. Interpreting and utilizing package vignettes and manuals, an often-overlooked…

I want to arrange the plot in a specific order. library(ggpubr) data(“ToothGrowth”) data(“mtcars”) mtcars$name <- rownames(mtcars) mtcars$cyl <- as.factor(mtcars$cyl) # create boxplot bxp <- ggboxplot(ToothGrowth, x = “dose”, y = “len”, color = “dose”, palette = “jco”) # create dotplot dp <- ggdotplot(ToothGrowth, x = “dose”, y = “len”, color…

# Program to connect points in a plot using ggplot # Load the required library library(ggplot2) # Define a function to connect points in a plot connect_points <- function(x, y) { tryCatch({ # Create a data frame with x and y coordinates data <- data.frame(x = x, y = y)…

# Program to Convert Bar Graph to Line Chart using ggplot # Load the required library library(ggplot2) # Function to convert bar graph to line chart convert_bar_to_line <- function(data, x, y) { # Check if the input data is a data frame if (!is.data.frame(data)) { stop(“Input data must be a…

Article Summary Box Preparing RStudio for package management is pivotal, involving setting up workspace directories and ensuring R version compatibility for optimal package functionality. In Understanding Package Libraries, the intricacies of library paths and package storage locations reveal strategies for streamlined package accessibility and organization. Advanced Techniques for Package Loading…

Article Summary Box RStudio’s Package Manager significantly simplifies the process of installing and managing R packages, enhancing user efficiency. CRAN’s vast repository offers a wide range of R packages, but understanding the nuances of package versions and dependencies is crucial for optimal utilization. Utilizing GitHub for R package installations opens…

Inclusion and ethics The DNA samples analysed in this project form part of a collection of biospecimens, including historically collected samples, maintained under Indigenous governance by the NCIG11 at the John Curtin School of Medical Research at the Australian National University (ANU). NCIG, a statutory body within ANU, was founded…

Cohorts Saliva and/or blood samples were collected from consenting individuals among four NCIG-partnered communities: Tiwi Islands (comprising the Wurrumiyanga, Pirlangimpi and Millikapiti communities), Galiwin’ku, Titjikala and Yarrabah, between 2015 and 2019. Non-Indigenous comparison data, generated from unrelated Australian individuals of European ancestry, was drawn from two existing biomedical research cohorts:…

I am working with data regarding dogs up for adoption in Washington and Oregon and wanted to see if the gender of the dogs has anything to do with their ability to be adopted. dput(dd_clean_df[1:10, ]) top_gender_breeds <- dd_clean_df %>% group_by(contact_state, breed_primary, sex) %>% summarise(count = n()) %>% arrange(contact_state, desc(count))…

I’m working on a project and have a scatterplot with Y axis as numerical ekg reading and X axis as the dates those reading were taken. My next step is to look at the data to within 1 year of pacemaker insertion and check if we have enough reading within…

I’ve conducted a DESeq2 analysis on a large volume of data and I’m trying to make box plots that compare the counts of specific genes, which are sorted into 2 groups, and include statistical significance. Using the plotCounts() function works fine, but I’m struggling to add the p.adj values calculated…

I have this code with dataframe that contain 20 cty groups. I wish to plot/assign to each specific cty value a color based on Wes Anderson color palettes (packages(“wesanderson”). Code: library(ggplot2) library(wesanderson) df <- mpg[, c(“displ”,”cyl”, “cty”, “hwy” )] df[-222,] pal <- wes_palette(20, name = “Zissou1”, type = “continuous”) ggplot(df,…

I am working with a dataset that I believe follows a “Negative Binomial” distribution. However, when I fit the Negative Binomial distribution, it turns out to be a poor fit. To explore further, I simulated a Negative Binomial distribution, but even on the simulated data, the overlaying distribution does not…

Let’s use the mtcars df and say we want to plot gseq density by cyl group (I don’t know what these things mean). I could use: ggplot(mtcars, aes(x=qsec, group=cyl, fill=as.factor(cyl))) + geom_density(adjust=1.5, alpha=.6, col= “black”) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank(), axis.line = element_line(colour = “black”))…

Article Summary Box Mastering the RStudio interface goes beyond basic navigation, involving strategic use of panes and shortcuts to streamline the coding process. Effective script organization significantly impacts readability and maintenance, emphasizing the role of modular structuring and clear documentation. In debugging and error handling, advanced techniques like conditional breakpoints…

Cancel Oops, something went wrong. Please try again in a few minutes. # This function creates a boxplot with a table of summary statistics using ggplot. # # PARAMETERS: # – data: A data frame containing the data to be plotted. # # – x: A character string specifying the…

Kraemer, M. U. et al. The global distribution of the arbovirus vectors Aedes aegypti and Ae. albopictus. Elife 4, e08347. doi.org/10.7554/eLife.08347 (2015). Article  PubMed  PubMed Central  Google Scholar  Bhatt, S. et al. The global distribution and burden of dengue. Nature 496, 504–507. doi.org/10.1038/nature12060 (2013). Article  ADS  CAS  PubMed  PubMed Central …

Steffen, W. et al. Planetary boundaries: guiding human development on a changing planet. Science 347, 1259855 (2015). Article  PubMed  Google Scholar  Kanter, D. R. et al. Nitrogen pollution policy beyond the farm. Nat. Food 1, 27–32 (2020). Article  ADS  Google Scholar  Tian, H. et al. A comprehensive quantification of global…

World Health Organization (WHO). WHO malaria report. 2022 www.who.int/publications/i/item/9789240064898 (2022). Savi, M. K. An overview of malaria transmission mechanisms, control, and modeling. Med. Sci. 11, 3 (2023). Google Scholar  Bahk, Y. Y. et al. Epidemiological characteristics of re-emerging vivax malaria in the Republic of Korea (1993–2017). Korean J. Parasitol. 56,…

I want to create a ggplot2 plot with multiple geom_rect objects. For now, I’m trying to create a plot with two geom_rect objects. I need segments of the x axis to be one of two “scales”. For example, the physical length between 0 and ten on the x axis might…

My plot background is much larger than the plot and I can’t figure out how to reduce it. I have hacked a way to bring the title closer to the plot, but there is still a large space below the plot. This causes issues when I use cowplot to place…

The code and approaches that I share here are those I am using to analyze TCGA methylation data. At the bottom of the page, you can find references used to make this tutorial. If you are coming from a computer background, please bear with a geneticist who tried to code…

Hi everybody, I’m trying to add brackets to show the p-values I obtained with a Tukey HSD test to show comparisons between each genotype in both levels of my treatment factor (e.g., comparing pks4-2 in DMSO and pks4-2 in NPA). I have looked online at the ggpubr package, but i…

Article Summary Box Customizing the RStudio Environment significantly boosts productivity, with options like project-specific settings and theme personalization enhancing the user experience. Advanced ggplot2 Techniques in data visualization offer a blend of aesthetics and functionality, enabling the creation of visually striking and informative plots. Efficient Data Management strategies in RStudio,…

You are interested in understanding more about the relationship between the age of a car and it’s value so that you can establish the right price to offer your customers. Create a scatterplot of value against. Add linear regression line without confidence intervals to the plot. A sample of the…

The solution is to explicitly call print() on ggplot object: library(ggplot2) p <- ggplot(mtcars, aes(wt, mpg)) p <- p + geom_point() print(p) ggplot function returns object of class ggplot; ggplot2 works by overloading print function to behave differently on objects of class ggplot – instead of printing them to STDOUT,…

removeBatchEffect with non-linear model fit 0 @2289c15f Last seen 6 hours ago Germany Hello, I am attempting to use limma’s removeBatchEffect for visualization purposes (heatmat & PCA) while fitting non-linear models (splines) to my expression data in DESeq2. Given that my design is balanced, would this approach work within the…

You can make the same plot with a fixed x axis as follows: library(ggplot2) library(ggtext) data.frame(word = rep(c(‘<i>Criptosporidium<br>parvum</i>’, ‘CSPV1’, ‘CSPV1 TLR3’), each = 2), n= c(69300,4858, 145, 6, 11, 0), Database = rep(c(‘Google Scholar’, ‘PubMed’), 3), check.names = FALSE) |> ggplot(aes(word, n)) + geom_col(aes(fill = Database), position = ‘dodge’) +…

Preamble Let’s say I have a function that allows users to create a boxviolin plot where box and violin plots are superposed. library(ggplot2) df <- dplyr::filter(mpg, class %in% c(“compact”, “midsize”)) p1 <- ggplot(df, aes(class, hwy)) + geom_violin() + geom_boxplot() p1 I also want to allow users to remove the violin…

I’m getting an error when I try to knit my .Rmd file. The code itself runs fine inside the file; the error only occurs when I try to knit. Quitting from lines 103-118 [unnamed-chunk-4] (Lab-14.Rmd) Warning messages: 1: In eng_r(options) : Failed to tidy R code in chunk ‘unnamed-chunk-2’. Reason:…

I’m working on creating a heatmap of objects in a shelving unit using RStudio. The way the shelving is configured IRL is one column is shelves #1-8 from top to bottom, next column is shelves #9-16 top to bottom, and so on, for 54 total shelving units, repeated for 6…

I am a beginner on R and I’ve tried and failed to create a stacked AND grouped barplot on RStudio. I managed to create grouped or stacked barplot as the basic barplot presented here with ggplot2 (r-graph-gallery.com/stacked-barplot.html), but I would like to have my 3 factors on the same graph,…