Tag: ggplot2

Reorder barplot in ggplot – tidyverse

Hi i want to reorder barplot according to class. This ggplot code does not appear in the order of classes when displayed as a plot. Can you please let me know what I am missing? families <- tibble::tribble(~supp, ~class, ~dose, ~len, ~sd,“CON”, “Firmicutes”, “Lachnospiraceae”, 4.97, 1.73,“CON”, “Bacteroidota”, “Bacteroidales RF16 group”,…

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Using element_ Textcustomize text in ggplot2

Ggplot2’s theme system allows us to better control graphicsNon data elementTo enhance the beauty of the image through more subtle modifications,Theme system of ggplot2Self contained multipleelement_function element_text( ) element_line( ) element_rect( ) element_blank( ) This section describes the topic element element_ Text (), which controls many parts of text elements…

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r – Can’t change ylab in ggplot

When I create this plot, I realize even I specify ylab, it is not applied to the output plot, whereas other labs works perfectly. Code below: saturation = function(po2,L){((po2/5.5)*(1+(po2/5.5))^3+ L*(po2/300)*(1+(po2/300))^3)/((1+(po2/5.5))^4+L*(1+(po2/300))^4)} #enter the equation library(ggplot2) library(ggtext) labels=”<p><span style=”color: #304d63;”>L = 10</span>, <span style=”color: #b2e7e8;”>L = 30</span>, <span style=”color: #8fb9aa;”>L = 100</span>,…

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Description, Programming Languages, Similar Projects of ggfx

ggfx is a (currently experimantal) package that allows the use of various filters and shaders on ggplot2 layers. Installation You can install ggfx from CRAN in the usual manner (install.packages(‘ggfx’)) or you can grab the development version directly from github using the devtools package: # install.packages(‘devtools’) devtools::install_github(‘thomasp85/ggfx’) Example The basic…

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R programming language tutorials – Technical Ripon

Are you learning the R programming language? Want to learn how to do more tasks with R? Check out our Do More With R video tutorials below — most with accompanying text articles and code, almost all under 10 minutes. In the table below you can easily search all tutorials…

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Bioconductor – sSNAPPY (development version)

DOI: 10.18129/B9.bioc.sSNAPPY     This is the development version of sSNAPPY; for the stable release version, see sSNAPPY. Single Sample directioNAl Pathway Perturbation analYsis Bioconductor version: Development (3.16) A single sample pathway pertrubation testing methods for RNA-seq data. The method propagate changes in gene expression down gene-set topologies to compute…

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How do I add a legend? I want to add legend to ggplot. please help me

How do I add a legend? I want to add legend to ggplot. please help me ka<-read.table(file = “K”,encoding= “UTF-8”,header = T) library(ggplot2) options(scipen=100) ka <- data.frame(aa = 2017:2020, bb = c(55550000,66660000,77770000,88880000), cc = c(12345,56789,23456,56756)) ggplot(ka, aes(aa)) + geom_col(aes(x=aa, y = bb/100), fill = “#F5513B”) + geom_line(aes(x=aa, y = cc))…

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r – Customize ggplot2 legend with different variables

I have the following data about American and German teenagers’ coding skills. I can easily display their bar plots, but I need to present the total number of teenagers from each country as well. DF <- data.frame(code = rep(c(“A”,”B”,”C”), each = 2), Freq = c(441,121,700,866,45,95), Country = rep(c(“USA”,”Germany”),3), Total =…

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r – change y axis scale in ggplot

I’m trying to replicate a plot drawn by graphpad in r but I have a problem changing the y axis here is an example data and my plot codes: library(ggplot2) data <- data.frame(names = rep(factor(LETTERS[1:3])), values = c(0.001, 0.02 ,0.95), group = rep(“A”,3)) ggplot(data, aes(x = group, y = values,…

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ggplot2 – R ggplot: how to change background per group of data points?

I am trying to ggplot my data in a forest plot-like fashion, and I would like to add a background for groups of datapoints like here: I know that for ggforest or survminer there are functions for this, but is there something like this in ggplot? If not background color,…

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Unicode Characters in ggplot2 PDF Output

As Ben suggested, cairo_pdf() is your friend. It also allows you to embed non-postscript fonts (i.e. TTF/OTF) in the PDF via the family argument (crucial if you don’t happen to have any postscript fonts that contain the glyphs you want to use). For example: library(ggplot2) cairo_pdf(“example.pdf”, family=”DejaVu Sans”) qplot(Sepal.Length, Petal.Length,…

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Visualizing Transcript Structure and Annotation using ‘ggplot2’ version 0.99.8 from GitHub

The goal of ggtranscript is the simplify the process of visualizing transcript structure and annotation. To achieve this, ggtranscript introduces 5 new geoms (geom_range(), geom_half_range(), geom_intron(), geom_junction() and geom_junction_label_repel()) as well as several helper functions. As a ‘ggplot2’ extension, ggtranscript inherits ‘ggplot2’s familiarity and flexibility, enabling users to intuitively adjust…

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Director of Bioinformatics in Chicago, IL for University of Chicago (UC)

Details Posted: 03-May-22 Location: Chicago, Illinois Type: Full-time Salary: Open Categories: Research – Laboratory/Non-Laboratory Staff/Administrative Location: Hyde Park Campus Job Description: Provides technical expertise in the selection, validation, and implementation of the appropriate internal and external data analytic and bioinformatic solutions needed to analyze specimens, process and integrate data, and…

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Error in SummarizedExperiment

I have installed DESeq2 version 1.36.0 samples <- colnames(txi$counts) group <- as.factor(c(“control”,”control”,”control”,”control”,”control”,”diet”,”diet”,”diet”,”diet”,”diet”, “control”,”control”,”control”,”control”,”control”,”diet”,”diet”,”diet”,”diet”,”diet”,”diet”)) coldata <- data.frame(samples, group, stringsAsFactors = F) coldata <- coldata[,c(“samples”,”group”)] coldata$samples <- factor(coldata$samples) coldata$group <- factor(coldata$group) rownames(coldata) <- sub(“fb”, “”, rownames(coldata)) all(rownames(coldata$samples) %in% colnames(txi)) all(rownames(coldata) == colnames(txi)) TRUE library(DESeq2) ddsTxi <- DESeqDataSetFromTximport(txi, colData = coldata, design =…

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ggplot2 – Plot two lines on one graph on left panel and their difference on the right panel using facet_wrap or facet_grid in R

I have the following data frames: df1 <- data.frame(a= c(1:10), x= c(0.1, 0.5, 0.2, 0.1, 0, 0.23, 0.25, 0.4, 0.01, 0.2), y= c(0.3,0.01, 0.8, 0.2, 0.02, 0.14, 0.47, 0.35, 0, 0.32), name=”L1″) df2 <- data.frame(a= c(1:10), x= c(0.2, 0.25, 0.2, 0.1, 0, 0.23, 0.25, 0.4, 0.01, 0.2), y= c(0.76,0.81, 0.18,…

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R For SEO Part 3: Data Visualisation With GGPlot2 & Wordcloud

[This article was first published on R | Ben Johnston, 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. R For SEO Part 3:…

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[Solved] ggplot with 2 y axes on each side and different

Sometimes a client wants two y scales. Giving them the “flawed” speech is often pointless. But I do like the ggplot2 insistence on doing things the right way. I am sure that ggplot is in fact educating the average user about proper visualization techniques. Starting with ggplot2 2.2.0 you can…

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Creating a non-stacked area plot in an easier way (ggplot2) : rprogramming

Hello! I don’t actually know what this type of chart would be called, but I essentially want to create a non-stacked area chart, ideally through one ggplot2 command. I’m able to create pretty much exactly what I’m after through simply calling geom_area() twice, as in the picture below. Here’s the…

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Learn to draw with Nature Genetics: a simple example of R language ggplot2 drawing a world map

Whole genome resequencing of 445 Lactuca access requests the household history of cultivated lettuce image.png The data of this paper is public. We can try to reproduce the graph used to display the data in the paper with the public data. The first figure uses a map to show the…

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r – Changing the order of a variable type displayed on ggplot

This is my first post so apologies if it is not explained in the best of ways, I will improve. I have created a line graph with ggplot2 that shows the number of cases for a specific disease per age category over a couple of months. df %>% ggplot(aes(x =…

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deseq2 problem

deseq2 problem 0 Hi I am trying to draw a PCA plot with DESeq2 but somehow I cannot use DESeq2 functions. It is a really simple code i wil be pasting below. > transform <- DESeq2::rlog(eliminated_data, blind = TRUE) Error in (function (classes, fdef, mtable) : unable to find an…

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19MID0006_AdcVis_Assessment-3.pdf – 19MID0006-UDHAYAKUMAR.P library(ggplot2) # Warning: package ‘ggplot2’ was built under R version 4.1.2 # Importing

19MID0006-UDHAYAKUMAR.Plibrary(ggplot2)## Warning: package ‘ggplot2’ was built under R version 4.1.2# Importing the datasetpikachu<-read.csv(“C:/Users/P.UDHAYAKUMARPERUMAL/Downloads/pokemon.csv”) head(pikachu)Name<chr>Type.1<chr>Type.2<chr>Total<int>HP<int>Attack<int>Defense<int>Sp..Atk<int>Sp..Def<int>1 BulbasaurGrassPoison31845494965652 IvysaurGrassPoison40560626380803 VenusaurGrassPoison5258082831001004VenusaurMega VenusaurGrassPoison625801001231221205 CharmanderFire30939524360506 CharmeleonFire40558645880656 rows | 1-10 of 13 columns(1)Categorical v/s Categorical(1.1)Stacked Barchart(Name v/s Type.1)df1<-ggplot(pikachu, aes(x = Name,fill = Type.1)) + geom_bar(position = “stack”) df1+theme(axis.text.x=element_text(angle=90))(1.2)Grouped Barchart(Type.1 v/s Type.2)df2<-ggplot(pikachu,aes(x = Type.1,fill = Type.2)) + geom_bar(position…

Continue Reading 19MID0006_AdcVis_Assessment-3.pdf – 19MID0006-UDHAYAKUMAR.P library(ggplot2) # Warning: package ‘ggplot2’ was built under R version 4.1.2 # Importing

Trimming the X axis for ggPlot – General

ggplot2 has good documentation here if you haven’t seen it: ggplot2.tidyverse.org Generate expansion vector for scales — expansion This is a convenience function for generating scale expansion vectors for the expand argument of scale_(x|y)_continuous and scale_(x|y)_discrete. The expansion vectors are used to add some space between the data and the…

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r – How to combine two qualitative data to make a bar graph

If you want to make two graphs to display Yesterday and Today in a single ggplot (or want to display both in the same plot) you’ll need to include a pivot_longer Example data df <- as.data.frame(structure(c(1L, 2, 3, 4, 5, 6, “Male”, “Female”, “Female”, “Male”, “Male”, “Female”, “Very good”, “Good”,…

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GitHub – mjfrigaard/ggplot2-graph-gallery: ggplot2 graph gallery

GitHub – mjfrigaard/ggplot2-graph-gallery: ggplot2 graph gallery This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed…

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Bioinformatics analysis identifies widely expressed genes

1Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China; 2Department of Pediatrics, The Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China Correspondence: Jun Qian, Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui,…

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How to Add Text to ggplot2 Plots (With Examples)

You can use the annotate() function to add text to plots in ggplot2. This function uses the following basic syntax: p + annotate(“text”, x=6, y=10, label= “hello”) where: x, y: The (x, y) coordinates where the text should be placed. label: The text to display. The following examples show how…

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GDCprepare of RNAseq counts produces error

GDCprepare of RNAseq counts produces error 1 @76ac7b25 Last seen 12 minutes ago Canada Hello everyone! I have been using the TCGAbiolinks package for the last couple years to access RNAseq data for the TCGA-LAML project. Just very recently, I had noticed that I could no longer use GDCquery to…

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Separate exogenous from endogenous transcripts using Salmon RNAseq DTU

Dear friends, We are trying to use Salmon for DTU analysis. We want to separate exogenous from endogenous transcripts by following this post www.biostars.org/p/443701/ and this paper f1000research.com/articles/7-952 We are focusing on a gene called ASCL1 (endo-ASCL1). We transduced cells with lentiviral vector containing ASCL1 ORF only (Lenti-ASCL1). There should…

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GDCquery_Maf error

GDCquery_Maf error 0 @76e1237b Last seen 1 day ago Singapore Hi all, I really need some help. I am trying to run GDCquery_Maf which worked fine until yesterday. Now I get the following error: Error in GDCquery(paste0(“TCGA-“, tumor), data.category = “Simple Nucleotide Variation”, : Please set a valid workflow.type argument…

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normal distribution – How can I plot multiple lines in ggplot2 in R?

How can I do this plot in ggplot2 form? transform this image to ggplot2 in R its code is mydata<-data.frame(alph=c(rep(c(0.01,0.05,0.1),each=6)),case=c(rep(c(“R”,”N”,”R”,”N”,”R”,”N”),each=3) ), Tests=c(rep(c(“SW”,”AD”,”LF”,”SW”,”AD”,”LF”,”SW”,”AD”,”LF”),each=1) ) , means=c(0.461,0.504,0.460,0.816,0.796,0.794, 0.619,0.650,0.602,0.630,0.602,0.620, 0.689,0.721,0.690,0.512,0.481,0.511)) x<-c(1,2,3) y1<-mydata[4][mydata[2]==”R” & mydata[3]==”AD”,] plot(x, y1, type = “l”, xaxt = “n”,ylim=c(0,1), xlab = “Alpha”, ylab = “Means”) axis(1, labels = as.character(c(0.01,0.05,0.1)), at…

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Histograms using ggplot2 within loop

I agree with @GabrielMagno, facetting is the way to go. But if for some reason you need to work with the loop, then either of these will do the job. library(gridExtra) library(ggplot2) df<-matrix(NA,2000,5) df[,1]<-rnorm(2000,1,1) df[,2]<-rnorm(2000,2,1) df[,3]<-rnorm(2000,3,1) df[,4]<-rnorm(2000,4,1) df[,5]<-rnorm(2000,5,1) df<-data.frame(df) out<-list() for (i in 1:5){ x = df[,i] out[[i]] <- ggplot(data.frame(x),…

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ggplot2 – Stacking Regression Plots from two separate locations in one study on R

For separate regression lines on the same plot/facet you can do this: ggplot(oceanregression, aes(x=log_phosphorus, y=chl.a_mg.m3, color=location))+ geom_point(col=”black”, size=2.5)+ xlab(“log phosphorus nmol/L”)+ ylab(“Concentration of Chl in mg/m3″)+ theme_classic()+ geom_smooth(method=lm, formula=y~x) If you want to have split into facets, you can do this: ggplot(oceanregression, aes(x=log_phosphorus, y=chl.a_mg.m3, color=location))+ geom_point(col=”black”, size=2.5)+ xlab(“log phosphorus nmol/L”)+…

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“Rprofile”to use rstudio on MAC

. rprofile againI received a comment at A recent post and taught me how to send command from R console to terminal using system functions.Used.As described above, the following is described in the console of the upper left corner of rstudio. library(stats) library(tidyverse) library(ggplot2) library(GGally) library(patchwork) library(lubridate) library(dplyr) We named…

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How best to output interactive ggplot graphs for screen size and readability like a normal ggplot? – General

Hello! I have this really simple plot example below using ggiraph to make it interactive. I have seen that this. You will see that in the example below we run gg_crime which is the ggplot version and finally the interactive one via girafe. My question is – how to best…

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ggplot2 – How To Update R Values

I have the below code which runs a 3 month picture of my metrics. I open the saved code, remove “Nov-21” and add “Feb-22”, then delete the first entry for each metric and add “Feb-22” entry to end of each metric (957L, 1208L, 1054L, 476L). Previously, the 3 month picture…

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Bioconductor Package Installation

When I try to install the gtf for hg38 BiocManager::install(“TxDb.Hsapiens.UCSC.hg38.knownGene”) I get the following error: ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01) Installing package(s) ‘TxDb.Hsapiens.UCSC.hg38.knownGene’ Error in readRDS(dest) : error reading from connection Per stackoverflow.com/questions/67455984/getoptionrepos-replaces-bioconductor-standard-repositories-see-reposito I…

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ggplot2 – R: Connecting Points in Arbitrary Order

This question already has answers here: Closed 13 hours ago. I am working with the R programming language. I generated the following random data set in R and made a plot of these points: library(ggplot2) set.seed(123) x_cor = rnorm(5,100,100) y_cor = rnorm(5,100,100) my_data = data.frame(x_cor,y_cor) x_cor…

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put the global variable(here is ‘var’) in the bolditalic string in ggtitle of ggplot using for loop – tidyverse

reference : r – How to use bold, italic and underline in ggplot2 – Stack Overflow Hi, I want to put the global variable(here is ‘var’) in the bolditalic string in ggtitle of ggplot using for loop. The graph doesn’t have a value corresponding to ‘var’, it just comes out…

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ggplot2 – Fail to plot by group on a phyloseq object generated by R package Divnet

Once you already have your phyloseq object df_family, you can use the function estimate_richness from phyloseq. You can then join the sample meta data to this data frame of alpha diversities. Finally, you can use ggplot2 directly to customize your plot accordingly, e.g. to put different sample groups (here SampleType)…

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Add Significance Level & Stars to Plot in R (Example)

  In this tutorial, I’ll demonstrate how to annotate significance levels to a ggplot2 plot using the ggsignif package in the R programming language. Table of contents: Here’s how to do it:   Example 1: Draw Boxplot with Significance Stars The following R code illustrates how to create a box-and-whisker…

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r – How can I make ggplot place ticks at the ends of an axis without manually specificly the ticks?

I am outputting a lot of figures in a loop where the y axis varies in scale and range. I noticed that in most instances the last tick is well before the end of the axis and the data often extends above this last tick. I’d like a programmatic way…

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Correctly place geom_text labels in forest plot with “fill” parameter in ggplot2 – General

Hi There, I want to create annotated publication-ready forest plots comparing different models. How do I ensure that the labels are placed above and tight against the corresponding error bars and do not overlap? Thank you for your help! Here is what I tried: library(tidyverse) #> Warning: package ‘tibble’ was…

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ggplot2loon function – RDocumentation

Examples # NOT RUN { if(interactive()) { p <- ggplot(mtcars, aes(wt, mpg)) + geom_point() g <- ggplot2loon(p) p1 <- ggplot(mtcars) + geom_point(aes(x = wt, y = mpg, colour = factor(gear))) + facet_wrap(~am) g1 <- ggplot2loon(p1) # } # NOT RUN { df <- data.frame( x = rnorm(120, c(0, 2, 4)),…

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Bioconductor – sccomp (development version)

DOI: 10.18129/B9.bioc.sccomp     This is the development version of sccomp; to use it, please install the devel version of Bioconductor. Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data Bioconductor version: Development (3.15) A robust and outlier-aware method for testing differential tissue composition from single-cell data. This model…

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quosure dplyr ggplot2 (1) – Code Examples

How to parametrize function calls in dplyr 0.7? The release of dplyr 0.7 includes a major overhaul of programming with dplyr. I read this document carefully, and I am trying to understand how it will impact my use of dplyr. Here is a common idiom I… …

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Pathway analysis of RNAseq data using goseq package

Hello, I have finished the RNA seq analysis and I am trying to perform some pathway analysis. I have used the gage package and I was looking online about another package called goseq that takes into account length bias. However, when I run the code I get an error. How…

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Function plot in ggplot incorrectly displayed as constant line-Tech Notes

Technical otaku 2022-03-08 I want to plot a high degree polynomial function with given coefficients.I created this functionf_erzeuger() is for writing a polynomial functionf to be able to use ggplot2 and stat_function(fun=f).coef is the coefficient vector of the polynomial function. f_erzeuger <- function(coef) { f <- function(x) { x_vec <-…

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How to Set the Number of Bins for a Histogram in ggplot2

You can use the bins argument to specify the number of bins to use in a histogram in ggplot2: library(ggplot2) ggplot(df, aes(x=x)) + geom_histogram(bins=10) The following examples show how to use this argument in practice. Example: Set Number of Bins for Histogram in ggplot2 The following code shows how…

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A Comprehensive Guide on ggplot2 in R

                                                                  Image source: Author       Introduction Visualization plays an important role in the decision-making process after analyzing relevant data. Graphical representation highlighting the interdependence of key elements affecting performance is important in the above process. There are many libraries in Python and R which provide different options showing…

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ggplot2 – Multiple Relative frequency histogram in R, ggplot

Below are some basic example with the build-in iris dataset. The relative part is obtained by multiplying the density with the binwidth. library(ggplot2) ggplot(iris, aes(Sepal.Length, fill = Species)) + geom_histogram(aes(y = after_stat(density * width)), position = “identity”, alpha = 0.5) #> `stat_bin()` using `bins = 30`. Pick better value with…

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rstudio::conf(2022) is open for registration!

rstudio::conf, the conference for all things R and RStudio, will take place July 25-28 in National Harbor, DC! As usual, we’ll have two days of workshops followed by two days of talks. If you’ve attended before and already know you want to attend, register now! Otherwise, read on to learn…

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Senior Bioinformatics Engineer, remote in Marlborough, MA at Quest Diagnostics

Look for more than answers. At Quest, we are on a continuous journey of discovery and development. It’s this attitude that has made us an industry leader and the #1 Diagnostic Lab in the US. For those joining us, we offer exciting and fast-moving career opportunities where you can affect…

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R: Sort VI.ggplot points list

R: Sort VI.ggplot points list sort.VIgraph {BrailleR} R Documentation Sort VI.ggplot points list Description Allows the list of data points listed by VI.ggplot to be sorted by x or y values, ascending or descending. Currently only implemented for geom_points. This function is experimental and has not been extensively tested. Usage…

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DESeq2 and high prefiltering cutoff

DESeq2 and high prefiltering cutoff 1 @255004b1 Last seen 3 hours ago United States Hi, I am curious about prefiltering with DESeq2. I understand from this site and reading the DESeq2 vignette that prefiletering is really unnecessary as DESeq2 has a stringent filtering that it does. However, I’m seeing better…

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Identification of Hub Genes Associated with COPD Through Integrated Bi

Introduction Chronic obstructive pulmonary disease (COPD) will become the third leading cause of death worldwide.1,2 The incidence of COPD worldwide is 13.1%3 and is 13.7% in the Chinese population over 40 years of age.4 Emphysema is one of the most common phenotypes.1 Over the past few decades, we have conducted…

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ggplot2 – In geom_text() how to shirnk text label size and not lost mapping attributes

In below code, I add text to plot using geom_text() and mapping value to the size. But the label size is a little big compare to plot, How to shrink all of them to little size ? (and not lost the mapping attributes).Thanks! library(tidyverse) plot_data <- data.frame(category=c(‘A’,’A’,’B’,’C’), sub_category=c(‘a1′,’a2′,’b1′,’c1’), value=c(6,12,3,2)) plot_data…

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Bioconductor – TAPseq

DOI: 10.18129/B9.bioc.TAPseq     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see TAPseq. Targeted scRNA-seq primer design for TAP-seq Bioconductor version: 3.12 Design primers for targeted single-cell RNA-seq used by TAP-seq. Create sequence templates for target gene panels and design gene-specific primers using…

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Bioconductor – branchpointer

DOI: 10.18129/B9.bioc.branchpointer     Prediction of intronic splicing branchpoints Bioconductor version: Release (3.14) Predicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs. Author: Beth Signal Maintainer: Beth Signal <b.signal at garvan.org.au> Citation (from within R,…

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Biostar Ggplot2

Showing : ggplot2 • reset updated 20 months ago by leahfa • 0 • written 20 months ago by yueli7 &utrif; 10 3.6 years ago Bogdan &utrif; 620 3.6 years ago zhe &utrif; 20 updated 3.9 years ago by TriS &utrif; 200 • written 3.9 years ago by da.de &utrif;…

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Validation of hub genes in acute pancreatitis

Introduction Acute pancreatitis (AP) is a common disease found in clinics, and requires urgent Hospital admission. The incidence of AP is increasing in recent years worldwide.1 The patients with AP increased from 1,727,789.3 to 2,814,972.3 between 1990 and 2019 in 204 countries and territories.2 Meanwhile, nearly 20% of AP patients…

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Introduction to ggplot2 with R – LibCal

Overview This is a hands-on workshop that covers how to use ggplot2 for common visualizations using the R programming language. It is not an introductory R programming workshop. See prerequisities below. Objectives In this workshop you will see how to use ggplot2 for: describing single variables and plotting simple…

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nf-core/circrna

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data Introduction nf-core/circrna is a best-practice analysis pipeline for the quantification, miRNA target prediction and differential expression analysis of circular RNAs in paired-end RNA sequencing data. The pipeline is built using Nextflow, a workflow tool to run tasks across…

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Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis

INTRODUCTION Next-generation sequencing (NGS) has revolutionized many areas of biological research (1, 2), providing ever-more data at an ever-decreasing cost. One such area is microbiome research, the study of microbes in their theater of activity using metagenomic sequencing (3). Here, deep short-read sequencing, and improving performance of long-read sequencing, are…

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ggplot2 – How can I directly compute a t-test for proportion in R from a data frame using prop_test?

I have a data frame with n>1000 in which each row includes data for columns Year, which is a numeric year, and Gender, which is either “Male” or “Female”. I want to compute a t-test for the proportion of Gender == “Male” pairwise between Years. I have succeeded in creating…

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r – ggplot2 running for minutes without plotting

I am attempting to plot the below vector, but when I run the function, it just continues to run and does not plot. I have waited 5 minutes before I feel uncomfortable and click stop in the console. Wondering what is going on. Up until this point I have had…

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r – trying to make a ggplot with two lines

The trick is to gather the columns you want to map as variables. As I don’t know, how you want to plot your graph, means, about x-axis and y-axis, I made a pseudo plot. and for your continuous variable part, you can either convert your values to integer or numeric…

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Bioconductor – OGRE (development version)

DOI: 10.18129/B9.bioc.OGRE     This is the development version of OGRE; to use it, please install the devel version of Bioconductor. Calculate, visualize and analyse overlap between genomic regions Bioconductor version: Development (3.15) OGRE calculates overlap between user defined genomic region datasets. Any regions can be supplied i.e. genes, SNPs,…

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Fatty infiltration after rotator cuff tear

Introduction Rotator cuff tear (RCT) is a common shoulder disorder causing shoulder pain and disability. The prevalence of full-thickness RCT is 20.7% in the general population, and increased with age.1 Rotator cuff play essential roles in shoulder function and the treatment of proximal humeral fractures.2,3 It is important to repair…

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Get ggplot2 Grapic observed versus estimated

R: Get ggplot2 Grapic observed versus estimated getggplot2GraphicObservadoXEstimado {Fgmutils} R Documentation Get ggplot2 Grapic observed versus estimated Description this function displays/saves/returns a Graphical ggplot2 illustrating the difference between the observed and estimated Usage getggplot2GraphicObservadoXEstimado(titulo = “observadoXestimado”, nome = “observadoXestimado”, observado, estimado, identificadorIndividual = NULL, identificadorGrupal = NULL, showTestF = TRUE,…

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use tcgabiolinks package to download TCGA data

TCGA Data download in terms of ease of use ,RTCGA The bag should be better , And because it’s already downloaded data , The use is relatively stable . But also because of the downloaded data , There is no guarantee that the data is new .TCGAbiolinks The package is…

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r – Is it possible to change a line from a ggplot/geom_line plot depending on what month the datapoint corresponds to?

Yes, it’s possible. The easiest way to do it by creating a vector of your colors, the same length as the rows in your dataframe, and passing it to the col argument in geom_line(). Here is an example: library(dplyr, warn.conflicts = FALSE) library(ggplot2) library(lubridate, warn.conflicts = FALSE) # create some…

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how to desnature legend ggplot2 code example

Example 1: labs fill ggplot2 df <- data.frame(x=1:10,group=c(rep(“a”,5),rep(“b”,5))) legend_title <- “OMG My Title” ggplot(df, aes(x=x, fill=group)) + geom_density(alpha=.3) + scale_fill_manual(legend_title,values=c(“orange”,”red”)) Example 2: labs fill ggplot2 p <- ggplot(df, aes(x=rating, fill=cond)) + geom_density(alpha=.3) + xlab(“NEW RATING TITLE”) + ylab(“NEW DENSITY TITLE”) p <- p + guides(fill=guide_legend(title=”New Legend Title”)) Read more here:…

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r – Displaying BIC and AICs from MSA nucleotide multisequence fasta file

I am trying to replicate MEGA (models/find best DNA protein models) using R. After reading R AICs and BIC documentation I can’t understand how I can implement it. How can I implement AICs and BICs without having to especify the number of sequences in the fasta file (in case that…

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r – How to plot average prices on a map in ggplot2

I am plotting home prices on a map using ggplot2. However, the outliers of really expensive homes is making all of the colors on my plot look the same so I was hoping to use the median house price instead. Below is what I have so for which includes the…

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Plotting greek letters and plain text in ggplot2 graphs via Rpy2

R’s expression() is taking objects, calls, or expression and returns an expression (that’s a way to manipulate unevaluated code). expression(“alpha”) returns the string “alpha” (like it would if writing in R expression(“alpha”). One way to get an expression is to parse a string. Using your example in the question that…

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Bioconductor – DaMiRseq (development version)

DOI: 10.18129/B9.bioc.DaMiRseq     This is the development version of DaMiRseq; for the stable release version, see DaMiRseq. Data Mining for RNA-seq data: normalization, feature selection and classification Bioconductor version: Development (3.15) The DaMiRseq package offers a tidy pipeline of data mining procedures to identify transcriptional biomarkers and exploit them…

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r – Ggplot2 legend with actual values instead of log

ProgrammerAnswered 1 days ago 0 I’ll start by loading the ggplot2 package. library(ggplot2) # v. 3.2.0 You can see I set a different color per fitted line. Since I’m setting these colors as constants this is done outside aes(). ggplot(mtcars, aes(mpg, hp) ) + geom_point() + geom_smooth(method = “lm”, se…

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r – Create a ggplot barplot with differently coloured horizontal rectangles as background

I like Allan Camerons approach best. Here is what I have tried to provide as an alternative using annotations: library(ggplot2) ggplot(data, aes(x=name, y=value))+ annotate(“rect”, xmin = 0.5, xmax = 4.5, ymin = 0, ymax = 5, fill = “red”, alpha = 0.2)+ annotate(“rect”, xmin = 0.5, xmax = 4.5, ymin…

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Profiling and functional characterization of maternal mRNA translation during mouse maternal-to-zygotic transition

INTRODUCTION Mammalian life starts with the fusion of two terminally differentiated gametes, sperm and oocyte, resulting in a totipotent zygote. After going through preimplantation development, the zygote reaches blastocyst before implantation. The two most important events taking place during preimplantation development are zygotic genome activation (ZGA) and the first cell…

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r – ggplot2 and grid.arrange, place legend below arranged plots

I am facing a problem when I arrange 2 ggplots next to each other using grid.arrange(). I want to place a legend evenly below both plots. So I have (pseudocode): p1 <- ggplot(data = df, aes(group = name, color=as.factor(fac), y = ys, x= (xs))) + geom_point() + geom_line() + theme(legend.position=”bottom”)…

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Color scales in ggplot2: I am completely lost

There are so many ways to define colour scales within ggplot2. After just loading ggplot2 I count 22 functions beginging with scale_color_* (or scale_colour_*) and same number beginging with scale_fill_*. Is it possible to briefly name the purpose of the functions below? Particularly I struggle with the differences of some…

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Turning off ggplot2 grids in rpy2

It is basically done the same way one would do it when using ggplot2 from R. Here is an example that turn off the grid intersecting with the X axis. More ways to “theme” a plot can be found in documentations and tutorials for ggplot2. from rpy2.robjects.lib.ggplot2 import ggplot, aes_string,…

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r – ggplot unable to fill plot by dataframe variable

I am attempting to plot a dataset and have the points filled dependent on a variable within the dataset; however, I am not getting the results I expected with the following code: library(ggplot2) #> Warning: package ‘ggplot2’ was built under R version 4.0.5 library(RColorBrewer) #> Warning: package ‘RColorBrewer’ was built…

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Bioconductor – STATegRa (development version)

DOI: 10.18129/B9.bioc.STATegRa     This is the development version of STATegRa; for the stable release version, see STATegRa. Classes and methods for multi-omics data integration Bioconductor version: Development (3.15) Classes and tools for multi-omics data integration. Author: STATegra Consortia Maintainer: David Gomez-Cabrero <david.gomezcabrero at ki.se>, Núria Planell <nuria.planell.picola at navarra.es>…

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Frequencies and characteristics of genome-wide recombination in Streptococcus agalactiae, Streptococcus pyogenes, and Streptococcus suis

1. Parte, A. C. LPSN–list of prokaryotic names with standing in nomenclature. Nucleic Acids Res. 42, D613-616 (2014). CAS  PubMed  Google Scholar  2. Krzyściak, W., Pluskwa, K. K., Jurczak, A. & Kościelniak, D. The pathogenicity of the Streptococcus genus. Eur. J. Clin. Microbiol. Infect. Dis. 32, 1361–1376 (2013). PubMed  PubMed…

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How to plot common y-axis text for combined figure (ggplot2)

I’m a beginner in R (and ggplot2). I’m trying to make 1×3 figure, and scale of y axis is same for all three figures. Also, I want to remove text and title of y axis for second and third plot. However, I realized that width of first figure become narrow…

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r – Where does ggplot set the order of the color scheme?

I think this is a reproducible example of what you’re seeing. In the diamonds dataset, the mean price of “Good” diamonds is actually higher than the mean for “Very Good” diamonds. library(dplyr) diamonds %>% group_by(cut) %>% summarize(mean_price = mean(price)) # A tibble: 5 x 2 cut mean_price <ord> <dbl> 1…

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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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