Tag: ggplot2

How to draw x and y axis in ggplot2 r? ( R, Ggplot2 )

Problem : ( Scroll to solution ) So, I’d like to draw x and y axis using ggplot2. I managed to draw x axis with a function: fun = function{x} {x* 0 }, but I don’t know how to do the same with y axis. If I use built in…

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Changing legend title in ggplot changes the shown legend aesthetic

I make some plot with ggplot2 like this: library(ggplot2) ggplot(df, aes(x, y, col= col)) + geom_point() Everything is good but as soon I set another legend title as shown here, the continuous colour gradient changes to some points in the legend: library(ggplot2) ggplot(df, aes(x, y, col= col)) + geom_point() +…

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ggplot2 – How to wrap graphs by categories while keeping the same width of bars with ggplot in R?

I am struggling with using facet_grid() and facet wrap() with ggplot(). I would like to be able to wrap the different stacked barcharts for every two categories (of the variable Department here) but at the same time have the same width of bars. The first action can be achieved with…

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r – ggplot two histograms in one plot

You can reference some of the other calculated values from stat functions using a notation that you may have seen before: ..value… I’m not sure the proper name for these or where you can find a list documented, but sometimes these are called “special variables” or “calculated aesthetics”. In this…

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ggplot2 – Create graphs by group using ggplot in R

I’m relatively new to using ggplot2 in R and have been struggling with this for awhile. I have figured out how to get everything from one data frame on a graph (that is pretty easy…), and how to write a loop function to get each observation (id in the example…

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Fixing abrupt changes/transitions in animated ggplot

I was wanting to make an animated ggplot of daily values for countries over the course of a year. I was able to do that thanks to some helpful questions/answers here. While the code below successfully makes a gif, the changes/transitions when countries move up or down/overtake one another is…

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Tabix file download error eQTL analysis

I am trying to download a tabix file to perform an analysis on an eQTL dataset, however I have the following error each each file I try to try from the eQTL – catalogue library(ggplot2) library(readr) library(coloc) library(GenomicRanges) library(seqminer) tabix_paths = read.delim(“https://raw.githubusercontent.com/eQTL-Catalogue/eQTL-Catalogue-resources/master/tabix/tabix_ftp_paths.tsv”, sep = “t”, header = TRUE, stringsAsFactors =…

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Plotting date intervals in ggplot2

I have a dataset which has a bunch of date intervals (i.e. POSIXct format start dates and end dates). In the example provided, let’s say it’s each period is associated to when someone was in school or out of school. I’m interested in plotting the data in ggplot2, each row…

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Theme text size vs. annotation text size. – ggplot2

A journal to which I am submitting a paper requires that all plot text, including annotation text, should be the same size. I recognize that the units for text size in the theme definitions (points as in font size) are different from the units for text size in annotations (mms)….

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Tutorial on Box Plot in ggplot2 with Examples – MLK

Introduction Boxplots are a useful visualization technique to understand the distribution and outliers in a dataset. In this article, we will go through the tutorial for box plot in ggplot2 function of R which is a popular visualization package. We will first understand the syntax of ggplot2 function geom_boxplot() for…

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ggplot2 – R knitr Markdown: Output Plots within For Loop

I am using child Rmd files in markdown, also works in sweave. in Rmd use following snippet: “`{r run-numeric-md, include=FALSE} out = NULL for (i in c(1:num_vars)) { out = c(out, knit_child(‘da-numeric.Rmd’)) } “` da-numeric.Rmd looks like: Variabele `r num_var_names[i]` ———————————— Missing : `r sum(is.na(data[[num_var_names[i]]]))` Minimum value : `r min(na.omit(data[[num_var_names[i]]]))`…

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Using logic in listcols (ggplot2 edition)

I am trying to produce a slightly different result from a purrr::map iteration depending on a condition. Say I have this code producing plots and storing them in a dataframe: library(tidyverse) #> — Attaching packages ————————————— tidyverse 1.3.1 — #> v ggplot2 3.3.5 v purrr 0.3.4 #> v tibble 3.1.6…

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Decimal digits in `Slope Graph` with `ggplot2`

Following a former question I opened few weeks ago: Slope Chart – ggplot2 I face another issue, concerning the numeric values reported in the graph. Even specifying the decimal digits I need (exactly 3) with any of the two commands: y=round(y, digit = 3) at the endof the code or…

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How to draw several lines with ggplot? ( R, Ggplot2 )

Problem : ( Scroll to solution ) This code draws 2 lines dd = list(data.frame(rates=1:5), data.frame(rates=2:6), data.frame(rates=3:7)) library(ggplot2) library(zoo) g = ggplot(, aes(1:5)) g <- g + geom_line(aes(y = dd[[1]]$rate[index(dd[[1]]) <= 5]), colour=”#000000″) g <- g + geom_line(aes(y = dd[[2]]$rate[index(dd[[2]]) <= 5]), colour=”#000000″) g But this code draws 1 line…

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Bioconductor – RiboCrypt

DOI: 10.18129/B9.bioc.RiboCrypt     Interactive visualization in genomics Bioconductor version: Release (3.14) R Package for interactive visualization and browsing NGS data. It contains a browser for both transcript and genomic coordinate view. In addition a QC and general metaplots are included, among others differential translation plots and gene expression plots….

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how to add colored tick label to ggplot2?

One option to add some colored squares beneath your colored labels would be via an additional geom_text layer. As the label I use a filled square with UTF-8 code “u25A0”. Using some fake random data to mimic your real data: library(ggplot2) ggplot(df, aes(x = Var2, y = Var1)) + geom_tile(fill…

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Ggplot: heatmap based on two vectors ( R, Ggplot2 )

Problem : ( Scroll to solution ) I am trying to plot data as a heat map in ggplot2. I understand that you’d normally have to have x, y, and z coordinated to plot x against y and then color by z. I have found plenty of heat map examples…

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Bioinformation Analysis Reveals IFIT1 as Potential Biomarkers in Centr

Introduction Tuberculosis (TB) is considered to be one of the top ten causes of death in the world, about a quarter of the world’s population is infected with M. tuberculosis.1 The World Health Organization (WHO) divides tuberculosis into pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (EPTB). Although breakthroughs have been made…

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ggplot2 – How to change the color of each facet in a scatter plot in R?

I’m trying to visualize two bivariate quantitative variables, disaggregated by the categorical variable stu_tech_cat. I would like each facet to have a different color, but have been unsuccessful in achieving that so far. Below is my code: tech_stu <- ggplot(mydata, aes(y = EEScore, x= subtct, fill = stu_tech_cat, color)) +…

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Bioconductor – derfinder (development version)

DOI: 10.18129/B9.bioc.derfinder     This is the development version of derfinder; for the stable release version, see derfinder. Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach Bioconductor version: Development (3.15) This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two…

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R-CoderDotCom | RCoderWeb – Github Help

R CODER’s Projects awesome-ggplot2 A curated list of awesome ggplot2 tutorials, packages etc. awesome-R A curated list of awesome R packages, frameworks and software. Awesome-R-packages A curated list 📄 of awesome 🌟 R packages 🌟 (WORK IN PROGRESS) calendR Ready to print calendars with ggplot2 chinchet A geom for adding…

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R ggpmisc::ggplot — EndMemo

R ggplot — ggpmisc ggplot() initializes a ggplot object. It can be used to declare the input spectral object for a graphic and to optionally specify the set of plot aesthetics intended to be common throughout all subsequent layers unless specifically overridden. ggpmisc::ggplot is located in package ggpmisc. Please install…

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Bioconductor – RDAVIDWebService

DOI: 10.18129/B9.bioc.RDAVIDWebService     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see RDAVIDWebService. An R Package for retrieving data from DAVID into R objects using Web Services API. Bioconductor version: 3.12 Tools for retrieving data from the Database for Annotation, Visualization and Integrated…

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r – Scatter plot with ggplot2

I am trying to make scatter plot with ggplot2. Below you can see data and my code. data=data.frame( gross_i.2019=seq(1,101), Prediction=seq(21,121)) ggplot(data=data, aes(x=gross_i.2019, y=Prediction, group=1)) + geom_point() This code produce chart below So now I want to have values on scatter plot with different two different colors, first for gross_i.2019 and…

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Bioconductor – TBSignatureProfiler (development version)

DOI: 10.18129/B9.bioc.TBSignatureProfiler     This is the development version of TBSignatureProfiler; for the stable release version, see TBSignatureProfiler. Profile RNA-Seq Data Using TB Pathway Signatures Bioconductor version: Development (3.15) Gene signatures of TB progression, TB disease, and other TB disease states have been validated and published previously. This package aggregates…

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Bioconductor – ChIPQC

    This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see ChIPQC. Quality metrics for ChIPseq data Bioconductor version: 3.1 Quality metrics for ChIPseq data Author: Tom Carroll, Wei Liu, Ines de Santiago, Rory Stark Maintainer: Tom Carroll <tc.infomatics at gmail.com>, Rory Stark <rory.stark…

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Data Visualization using Plotnine and ggplot2 in Python

  Data Visualization is the technique of presenting data in the form of graphs, charts, or plots. Visualizing data makes it easier for the data analysts to analyze the trends or patterns that may be present in the data as it summarizes the huge amount of data in a simple…

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ggplot2 and cumsum() – Stackify

Here’s a test data which uses plyr‘s transform to calculate the cumulative sum first and then apply that data to plot using ggplot2: set.seed(45) DF <- data.frame(grp = factor(rep(1:5, each=10)), x=rep(1:10, 5)) DF <- transform(DF, y=runif(nrow(DF))) # use plyr to calculate cumsum per group of x require(plyr) DF.t <- ddply(DF,…

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ggplot function error – General

So I have been trying to visualize my data using ggplot. I used the following command: ggplot(data = inv_database, mapping= aes(x = Gender,y = Total.Monthly.Income))+ geom.point(size=5)+ geom.line(colour=”red”) The response I am getting; Error in ggplot(data = inv_database, mapping = aes(x = Gender, y = Total.Monthly.Income)) : could not find function…

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r – How to plot a bar plot by ggplot2 and sort bars in non-alphabetical order

This question already has answers here: Closed 11 hours ago. I’m trying to plot a boxplot by ggplot2 and it sorts the boxes in alphabetical order, but I want to change their order. How can I do that? Thanks for any help. Here is my code:…

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Multiple data points in one r ggplot2 plot ( R, Ggplot2 )

Problem : ( Scroll to solution ) I have two sets of data points that both relate to the same primary axis, but who differ in secondary axis. Is there some way to plot them on top of each other in R using ggplot2? What I am looking for is…

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[R] question about for loop

y, c, and f only exist in the context of mac2 If you want to use them, you’ll have to write mac2$y, mac2$c, or mac2$f (or the [[ versions mac2[[“y”]], mac2[[“c”]], or mac2[[“f”]]) Combining that with index i would then look like mac2$y[[i]] or mac2[[i, “y”]] Also, I think you…

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R ggtree: How to label single tree tip with ggtree similar to labeling nodes with geom_cladelabel

I’m having trouble with labeling single tips in my tree with ggtree. I’m trying to highlight and label nodes from a tree with geom_hilight and geom_cladelabel. This seems to work fine with nodes that have more than 1 tree tip, but when I try to label a single tip, I…

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Custom ggplot2 axis and label formatting

You can set the prefix in dollar_format for euros instead of dollars: scale_y_continuous(labels=dollar_format(prefix=”€”)) + That takes care of the scientific notation issue. To get everything in thousands, you could just divide by 1000 when you create the summary. To reduce clutter, you could leave out the euro symbol in the…

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r – Avoiding eval-parse or do.call

I am trying to select a theme from ggplot2 based on some string given. For demo purposes, consider the following code: library(dplyr); library(ggplot2) mtcars %>% ggplot(aes(mpg, wt))+ geom_point() -> p all_ggplot2_funs <- getNamespaceExports(“ggplot2”) p + eval(parse(text=paste0(all_ggplot2_funs[grep(“theme_”, all_ggplot2_funs)][15], “()”))) This works fine and would allow me to use theme_minimal. However, from…

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ggplot2 – R ggplot – ploting multiple variables with sub-categories in the same plot with two axes

I have this data: date area people_tested positive_cases positive 2021-12-09 Total 76282.0 402.0000 0.005300000 2021-12-10 Total 84023.0 389.0000 0.004600000 2021-12-09 Total_3da NA 382.3333 0.004900000 2021-12-10 Total_3da NA 377.6667 0.004933333 2021-12-09 Paris_3da 75257.4 NA NA 2021-12-10 Paris_3da 71553.6 NA NA and I would like to create a plot with a line…

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Bioconductor – ProteoDisco

DOI: 10.18129/B9.bioc.ProteoDisco     Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences Bioconductor version: Release (3.14) ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (mutant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript…

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[R] FinCal and ggplot2 packages in r could not be loaded.

Hello R users community, I installed ‘FinCal’ and ‘ggplot2’ packages in r and tried to load them, but I couldn’t load them. R gave me the following error. >library(FinCal) Error: package or namespace load failed for ‘FinCal’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package…

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r – How to draw boxplot by multiple groups using ggplot2?

I try to get a boxplot with the following specifications for the following variables: assets, liability. My data is firms financial statement and firms are classified big and small firms (categorical variable lbg30). Time (years) is also categorized by two period pre-crisis and post-crisis (categorical variable postcrisis). So I want…

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ggplot: remove lines at ribbon edges

You can remove the border using the colour argument: ggplot(d, aes(Time, y, color = Object, fill = Object)) + geom_line(size = 2) + geom_ribbon(aes(ymin = lower, ymax = upper), alpha = .3, colour = NA) geom_ribbon understands linetype aesthetic. If you want to map linetype to a variable include it…

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r – ggplot2 Set geom_point Size according to a Factor

I am trying to set the size of geom_point according to a factor. I know it is not advised, but my data is extremely unbalanced (the minimum value is 6 while the maximum is larger than 10,000). I am trying to make the size of the points reflect the total…

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Draw Cumulative Histogram in R (Example)

  In this R tutorial you’ll learn how to draw the cumulative sum of a vector in a histogram. Table of contents: Here’s how to do it!   Example Data The following data is used as basement for this R programming language tutorial: set.seed(258967) # Create example data data <-…

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GitHub – z3tt/hands-on-ggplot2

GitHub – z3tt/hands-on-ggplot2 You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. Read more here: Source link

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r – Geom_text not legible with greater values using ggplot2

While creating a ggplot2 graph using geom_text, the text is legible as long as the y values are somehow within the same range. (y limits = 121) However, when I add a new variable with a greater range, the text is illegible (y limits = 271) This is the code…

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Adding numbers and characters to legend key in ggplot2 of UMAP clusters

Adding numbers and characters to legend key in ggplot2 of UMAP clusters 0 Hi everyone, I have a UMAP cluster, however there are so many clusters that the descriptions look clunky if i put them on the umap…but then there are too many colors if it just colors. So, i…

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xlim not working for discrete values [ggplot2]

I’m trying to set xlim and ylim in ggplot put using the below: ylim=c(0, 1.5) + xlim=c(0,100) + OR coord_cartesian(xlim = c(0, 100), ylim = (0,1.5)) + Seems to throw this error: Error in scale_x_discrete(breaks = c(0, 50, 100), labels = c(0, : non-numeric argument to binary operator Is this…

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[Solved] R Alignment of images in tables with markdown, rstudio and knitr

I’m trying to create a standard monthly report for work in PDF format using Rstudio and I want to incorporate ggplot output with a table of figures – a new chart, one per cell on each row. I’m new to markdown, latex, pandoc and knitr so this is a bit…

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#30DayMapChallenge: The good, the bad and the ugly of crafting maps with ggplot2

About the instructor:Dr. Cédric Scherer is a graduated computational ecologist with a passion for design. In 2020, he combined his expertise in analyzing and visualizing large data sets in R with his passion to become an freelance data visualization specialist. Cédric has created visualizations across all disciplines, purposes, and styles…

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FAQ: Intro to Visualization with R – The ggplot() function – Uncategorized

This community-built FAQ covers the “The ggplot() function” exercise from the lesson “Intro to Visualization with R”. Paths and CoursesThis exercise can be found in the following Codecademy content: Analyze Data with R Learn RLearn ggplot2 FAQs on the exercise The ggplot() function There are currently no frequently asked questions…

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Merge and Perfectly Align Histogram and Boxplot using ggplot2

since yesterday I am reading answers and websites in order to combine and align in one plot an histogram and a boxplot generated using ggplot2 package. This question differs from others because the boxplot chart needs to be reduced in height and aligned to the left outer margin of the…

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r – ggplot2 vertical colorbar title right centered

Here is a solution, inspired in this SO post.Note that in the question you have fill = guide_colourbar(.) when it should be colour = guide_colourbar(.). library(ggplot2) ggplot(df, aes(x=img_type, y=metric),show.legend = FALSE) + geom_point(aes(size = abs_corr, colour=corr))+ scale_size(range =c(-0.1,20) )+ scale_colour_gradient2( low = “#7e1952”, high = “#2f7a9a”, space = “Lab”, na.value…

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Annotate Rotated Text Label to ggplot2 Graph in R (Example Code)

This page demonstrates how to add a rotated text label to a ggplot2 graphic in R programming. Preparing the Example data(iris) # Example data head(iris) # Sepal.Length Sepal.Width Petal.Length Petal.Width Species # 1 5.1 3.5 1.4 0.2 setosa # 2 4.9 3.0 1.4 0.2 setosa # 3 4.7 3.2 1.3…

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r – Where can I find documentation on the `..*..` ggplot options?

Here are all of the ..*.. options mentioned in the ggplot2 help files (or at least those help files that can be brought up by typing ?”<func>”, where “<func>” refers to one of the functions exported by ggplot2). library(ggplot2) ## Read all of the ggplot2 help files and convert them…

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Bioconductor – MSstats

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see MSstats. Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments Bioconductor version: 3.4 A set of tools for statistical relative protein significance analysis in DDA, SRM and DIA…

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Break on x and y axis on a ggplot – General

Hi, I get some data from an experiment that I would like to plot with ggplot2.The problem I have is that both measures have a huge difference. To make it more appreciable, I would like to set axis break on x and y axis for the same plot.I found the…

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r – Two plots within one facet in ggplot2

I have two types of data to create two types of plot, bar and line. They have different y axis, but same x axis. They are each categorized by the same category levels Example Code: data <- data.frame( Station = sample(LETTERS[seq( from = 1, to = 4 )],50, rep =…

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Expression in ggplot2 facet labels

I would like to have an R expression in a ggplot2 facet label. Let’s say I’m plotting the tips data.frame: library(reshape2) > head(tips) total_bill tip sex smoker day time size 1 16.99 1.01 Female No Sun Dinner 2 2 10.34 1.66 Male No Sun Dinner 3 3 21.01 3.50 Male…

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Design formula in DESeq2

Hello, I am using DESeq2 for analysis of RNAseq data. I would like to ask you about the design in the DESEq2 formula. I have tissue from animals treated with a chemical and my animal model is a colorectal cancer model. My variables are gender (male or female), treatment (treated…

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making y-axis labels bold in ggplot (x-axis is set bold but y-axis label doesn’t change)

making y-axis labels bold in ggplot (x-axis is set bold but y-axis label doesn’t change) I am trying to set axis labels and ticks bold in ggplot but y-axis labels is not setting to bold. Please suggest what I should add to the script. Below is a reproducible example. I…

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r – Position Trend line regression equation in ggplot

i am trying to plot trend lines equation with R square for three variable (SA,SA1,SA2) using ggplot geom_smooth(). While plotting three variables i get overlapping equation. I tried to adjust the y lab position using stat_regline_equation(label.y = c(1.78e15,3.9e17,2.5e15)) but miserably failed in doing so. DATA LINK (Requirement: 3 trend lines…

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Bioconductor – Rariant

    This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see Rariant. Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies Bioconductor version: 3.0 The ‘Rariant’ package identifies single nucleotide variants from sequencing data based on the difference of…

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Adjust the legends distance to the x-axis?

ggplot2: Adjust the legends distance to the x-axis? I want to shrink the legends distance to the x-axis, but I can’t find a way to do it. Is it possible? Example code: library(ggplot2) ggplot(mtcars, aes(x = gear, y = mpg, fill = gear)) + geom_bar(stat = “identity”) + theme(legend.position =…

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Transparency and Alpha levels for ggplot2 stat_density2d with maps and layers in R

Transparency and Alpha levels for ggplot2 stat_density2d with maps and layers in R Can anyone offer suggestions as to the best way to deal with transparency and alpha levels with many layers (with reference to ggplot2)? In the sample code below, it becomes very difficult to see individual state borderlines…

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README

README ggmatplot is a quick and easy way of plotting the columns of two matrices or data frames against each other using ggplot2. Overview ggplot2 requires wide format data to be wrangled into long format for plotting, which can be quite cumbersome when creating simple plots. Therefore, the motivation for…

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Bioconductor – interactiveDisplay

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see interactiveDisplay. Package for enabling powerful shiny web displays of Bioconductor objects Bioconductor version: 3.2 The interactiveDisplay package contains the methods needed to generate interactive Shiny based display methods for Bioconductor objects. Author: Shawn…

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ggplot, drawing multiple lines across facets

ggplot, drawing multiple lines across facets I drew two panels in a column using ggplot2 facet, and would like to add two vertical lines across the panels at x = 4 and 8. The following is the code: library(ggplot2) library(gtable) library(grid) dat <- data.frame(x=rep(1:10,2),y=1:20+rnorm(20),z=c(rep(“A”,10),rep(“B”,10))) P <- ggplot(dat,aes(x,y)) + geom_point() +…

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AYUSH_MALAKAR_HW6.doc – Course IST 687 Assignment HW 6 Name Ayush Malakar Date library’ggplot2#including package#Step-1 AQ_dataset

################################################ Course: IST 687# Assignment: HW 6# Name: Ayush Malakar# Date: 08/17/2021# ###############################################library(‘ggplot2’) #including package#Step-1AQ_dataset<- airquality #loading the dataset into a new variable#Step-2AQ<- na.omit(AQ_dataset) #removing NA’s from the dataset#Step-3 (1)#1x <- ggplot(AQ, aes(x=Ozone)) #defining plot and aestheticsx<- x+geom_histogram(bins =5, colour=’black’, fill=’white’) # defining the shape and structure of the histogramx…

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CRAN – Package ggmatplot

CRAN – Package ggmatplot ggmatplot: Plot Columns of Two Matrices Against Each Other Using ‘ggplot2’ A quick and easy way of plotting the columns of two matrices or data frames against each other using ‘ggplot2’. Although ‘ggmatplot’ doesn’t provide the same flexibility as ‘ggplot2’, it can be used as a…

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AYUSH_MALAKAR_HW9.doc – Course IST 687 Assignment HW 9 Name Ayush Malakar Date#library library”kernlab library”ggplot2 library”e1071

############################################### # Course: IST 687 # Assignment: HW 9 # Name: Ayush Malakar # Date: 09/09/2021 # ############################################### #library library(“kernlab”) library(“ggplot2”) library(“e1071”) library(“gridExtra”) #Step 1: Load the data airquality #replacing NA’s with mean values airquality$Ozone[is.na(airquality$Ozone)] <- round(mean(airquality$Ozone, na.rm = TRUE)) airquality$Solar.R[is.na(airquality$Solar.R)] <- round(mean(airquality$Solar.R, na.rm = TRUE)) airquality #Step 2: Create…

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Edmonton R User Group Meetup: ggplot2 intro

This month we’re going to be a little more hands-on! Marcus Becker will walk through a new Tidy Tuesday dataset, show some basic data exploration techniques, and go over some ways to visualize the data in ggplot2. The hope is that this session will be useful for newcomers to ggplot2,…

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Boxplot (ggplot2) not working as expected

I’m trying to plot a simple boxplot where I get 15 boxplots for respondents age of 15 “Cadernos” (15 surveys, surveys A, B, C .. to O). But that’s not working as expected. I have already tried to switch places to the “Cadernos” (surveys) and “Idade” (age) variables. Any idea?…

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Data visualization with R and ggplot2

ggplot2 package in R Programming Language also termed as Grammar of Graphics is a free, open-source, and easy-to-use visualization package widely used in R. It is the most powerful visualization package written by Hadley Wickham. It includes several layers on which it is governed. The layers are as follows: Building…

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r – Creating a graph to show values for different groups

Here is a small example how you could apply tidyr::pivot_longer and ggplot to create the desired graph. library(ggplot2) data <- data.frame(age= c(“16-24”, “25-34”, “35-44”, “45-54”), “y2014” = c(100,200,300,400), “y2015” = c(250,350,450,550), “y2016” = c(240, 340,440,550)) dataLong <- tidyr::pivot_longer(data, cols=c(“y2014”, “y2015”, “y2016”)) dataLong$year <- as.numeric(sub(“.”, “”, dataLong$name)) ggplot(dataLong) + geom_point(aes(x=year, y=value,…

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ggplot2 each group consists of only one observation-plotting two lines on one graph

Beginner R user here. I am trying to graph two simple lines using the following data frame: date_of_case <- c(“7/12/2020”, “7/13/2020”, “7/14/2020”, “7/15/2020”, “7/16/2020”, “7/17/2020”, “7/18/2020”, “7/19/2020”, “7/20/2020”, “7/21/2020”, “7/22/2020”, “7/23/2020”, “7/24/2020”, “7/25/2020”, “7/26/2020”, “7/27/2020”, “7/28/2020”, “7/29/2020”, “7/30/2020”, “7/31/2020”, “8/01/2020”, “8/02/2020”, “8/03/2020”) Masked <- c(25, 23, 20, 20.5, 20, 20,…

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r – ggplot: multiple time periods on same plot by month

I am trying to plot multiple time-periods on the same time-series graph by month. This is my data: pastebin.com/458t2YLg. I was trying to avoid dput() example but I think it would have caused confusion to reduce the sample and still keep the structure of the original data. Here is basically…

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Data Science: R Basics | Harvard University

Course description The first in our Professional Certificate Program in Data Science, this course will introduce you to the basics of R programming. You can better retain R when you learn it to solve a specific problem, so you’ll use a real-world dataset about crime in the United States. You…

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r – How to add multiple arrows to a path according to line direction using ggplot2?

I have a data frame that I want to plot a path from. The data frame also indicates the direction the arrows should have. I have been using the ggplot2 package and the geom_path() function for this, however, I want to add arrows that indicate the direction of the path….

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SeuratTheme function – RDocumentation

Usage SeuratTheme()CenterTitle(…)DarkTheme(…)FontSize( x.text = NULL, y.text = NULL, x.title = NULL, y.title = NULL, main = NULL, … )NoAxes(…, keep.text = FALSE, keep.ticks = FALSE)NoLegend(…)NoGrid(…)SeuratAxes(…)SpatialTheme(…)RestoreLegend(…, position = “right”)RotatedAxis(…)BoldTitle(…)WhiteBackground(…) Examples # NOT RUN { # Generate a plot with a dark theme library(ggplot2) df <- data.frame(x = rnorm(n = 100, mean…

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r – different color scales for same aesthetic in different layers in ggplot2, without unstable packages

is it possible to have multiple color scales for different layers? I emulated what I would like to archive by using a fill aesthetic for a geom_point with shape=21 in the example below. library(tidyverse) test <- tibble( x=c(1:4, 1:4), y=c(1:4, 2:5), a=factor(c(“a”, “a”, “b”, “b”, “a”, “a”, “b”, “b”)), A=factor(c(“A”,…

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TCGA dataset normalization

TCGA dataset normalization 0 hi. i am new to machine learning. i want to normalize my data which I downloaded from UCSC Xena browser for pancreatic cancer TCGA PAAD is its id. when I try to run this code it is showing error given below library( “DESeq2” ) library(ggplot2) countData…

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Problem with Risk table in Kaplan-Meier plot

Hi everybody! It is my first time here and I wish to as clear and kind as every user in this forum. I am trying to generate a Kaplan-Meier Plot for Overall Survival using survival and ggplot2 packages, with the data contained in data1. OS variable codifies time variable and…

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miRNAs and mRNAs in intestinal ischemia-reperfusion injury

Introduction Intestinal ischemia-reperfusion (II/R) injury is a severe clinical complication common in the Intensive Care Unit (ICU). It is associated with high morbidity and mortality.1 Usually, this problem is followed by various causes, including sepsis, shock, trauma, and so on.2 Intestinal ischemia-reperfusion injury destroys intestinal tissue and impairs the function…

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Bioconductor – ERSSA

DOI: 10.18129/B9.bioc.ERSSA     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ERSSA. Empirical RNA-seq Sample Size Analysis Bioconductor version: 3.9 The ERSSA package takes user supplied RNA-seq differential expression dataset and calculates the number of differentially expressed genes at varying biological replicate…

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Bioconductor – NBAMSeq

DOI: 10.18129/B9.bioc.NBAMSeq     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see NBAMSeq. Negative Binomial Additive Model for RNA-Seq Data Bioconductor version: 3.9 High-throughput sequencing experiments followed by differential expression analysis is a widely used approach to detect genomic biomarkers. A fundamental step…

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Phylogeographic reconstruction of the marbled crayfish origin

Procambarus fallax collections and PCR genotyping Animals were collected from various wild populations (Table S1) in compliance with state and local regulations (Georgia department of natural resources scientific collection permit 115621108, state of Florida collection permits S-19-10 and S-20-04). DNA was isolated from abdominal muscle tissue using SDS-based extraction and precipitation…

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Bioconductor – FunciSNP

DOI: 10.18129/B9.bioc.FunciSNP     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see FunciSNP. Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs Bioconductor version: 3.11 FunciSNP integrates information from GWAS, 1000genomes and chromatin feature to identify functional SNP in…

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How to output MDS plot for RNAseq samples with ggplot2?

Dear all. I am trying to output an MDS plot to understand the relationship between RNAseq data. I was able to output the MDS plot using “diffExpr.P0.001_C2.matrix” output by edgeR. However, I would like to use ggplot2 to output it in a more readable form. I have tried the following…

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Bioconductor – TBSignatureProfiler

DOI: 10.18129/B9.bioc.TBSignatureProfiler     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see TBSignatureProfiler. Profile RA-Seq Data Using TB Pathway Signatures Bioconductor version: 3.12 Signatures of TB progression, TB disease, and other TB disease states have been created. This package makes it easy to…

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Bioconductor – GEOexplorer (development version)

DOI: 10.18129/B9.bioc.GEOexplorer     This is the development version of GEOexplorer; to use it, please install the devel version of Bioconductor. GEOexplorer: an R/Bioconductor package for gene expression analysis and visualisation Bioconductor version: Development (3.14) GEOexplorer is a Shiny app that enables exploratory data analysis and differential gene expression of…

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Bioconductor – PPInfer

DOI: 10.18129/B9.bioc.PPInfer     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see PPInfer. Inferring functionally related proteins using protein interaction networks Bioconductor version: 3.12 Interactions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated…

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Bioconductor – GRENITS

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see GRENITS. Gene Regulatory Network Inference Using Time Series Bioconductor version: 2.14 The package offers four network inference statistical models using Dynamic Bayesian Networks and Gibbs Variable Selection: a linear interaction model, two linear…

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Bioconductor – ramr

DOI: 10.18129/B9.bioc.ramr     Detection of Rare Aberrantly Methylated Regions in Array and NGS Data Bioconductor version: Release (3.13) ramr is an R package for detection of low-frequency aberrant methylation events in large data sets obtained by methylation profiling using array or high-throughput bisulfite sequencing. In addition, package provides functions…

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Finding the significance of the overlap between 2 or more gene sets using simulation in R.

TLDR: Example R function to calculate significance of overlap of 2 or more gene sets. genes_all is a vector that contains all genes, and gene_sets takes a list of vectors for each gene set. I encourage people to read the full tutorial and attempt to reproduce the code themselves (especially…

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Outliers on DESEq2 Results

I have an RNAseq dataset, where one of the genes I intend to analyze has hundreds of counts ranging from 10 to 12, with a few counts > 9000. I process this data in Deseq2 and get that the gene is differentially expressed across several samples of interest. What can…

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Transitional genomes and nutritional role reversals identified for dual symbionts of adelgids (Aphidoidea: Adelgidae)

1. Szathmáry E, Smith JM. The major evolutionary transitions. Nature 1995;374:227–32. PubMed  Google Scholar  2. West SA, Fisher RM, Gardner A, Kiers ET. Major evolutionary transitions in individuality. Proc Natl Acad Sci USA. 2015;112:10112–9. CAS  PubMed  PubMed Central  Google Scholar  3. Moran NA. The coevolution of bacterial endosymbionts and phloem-feeding…

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Is there a way to convert “dist” to “data.frame”?

Is there a way to convert “dist” to “data.frame”? 1 Hi, all. I will output MDS plot with ggplot2. But, I couldn’t read the data because the class of the data wasn’t support in ggplot2. Is there a way to convert “dist” to “data.frame”? Although I tried “as.data.frame()“, I was…

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Bioconductor – conclus

DOI: 10.18129/B9.bioc.conclus     ScRNA-seq Workflow CONCLUS – From CONsensus CLUSters To A Meaningful CONCLUSion Bioconductor version: Release (3.13) CONCLUS is a tool for robust clustering and positive marker features selection of single-cell RNA-seq (sc-RNA-seq) datasets. It takes advantage of a consensus clustering approach that greatly simplify sc-RNA-seq data analysis…

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Bioconductor – FoldGO

DOI: 10.18129/B9.bioc.FoldGO     Package for Fold-specific GO Terms Recognition Bioconductor version: Release (3.13) FoldGO is a package designed to annotate gene sets derived from expression experiments and identify fold-change-specific GO terms. Author: Daniil Wiebe <daniil.wiebe at gmail.com> [aut, cre] Maintainer: Daniil Wiebe <daniil.wiebe at gmail.com> Citation (from within R,…

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Bioconductor – traviz (development version)

DOI: 10.18129/B9.bioc.traviz     This is the development version of traviz; to use it, please install the devel version of Bioconductor. Trajectory functions for visualization and interpretation. Bioconductor version: Development (3.14) traviz provides a suite of functions to plot trajectory related objects from Bioconductor packages. It allows plotting trajectories in…

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