Tag: ggplot2

r – Writing a fuction to Automate Repetitive Plotting in ggplot2

A great way to iterate over a list with a particular function would be to use lapply(). Here is an example that should demonstrate the concept. library(ggplot2) # data frames put into a list d1 <- data.frame(x=1:10, y=1:10) d2 <- data.frame(x=1:100, y=(1:100)^2) d3 <- data.frame(x=1:200, y=log(1:200)) mylist <- list(d1, d2,…

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ggplot2 – remove NA’s from only one Variable in scatter plot with 2 variables over time in R / ggplot

I want to plot 2 variables over a time period with ggplot. One of the variables contains NAs. I want to drop the NAs from the plot without losing the value for the other variable. Right now, ggplot plots all NAs in a line at the top of the y-axis….

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Bioconductor – EasyCellType

DOI: 10.18129/B9.bioc.EasyCellType     Annotate cell types for scRNA-seq data Bioconductor version: Release (3.16) We developed EasyCellType which can automatically examine the input marker lists obtained from existing software such as Seurat over the cell markerdatabases. Two quantification approaches to annotate cell types are provided: Gene set enrichment analysis (GSEA)…

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lazy loading failed, unable to load shared object rtracklayer.so

Hello! I am working on analyzing a dataset I created with the 10x Chromium Single Cell Multiome kit. In order to add gene annotation to the ATAC data, I am trying to install and use the “EnsDb.Mmusculus.v79” and “BSgenome.Mmusculus.UCSC.mm10” packages with bioconductor. The same ERROR has come up repeatedly whenever…

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Solved Use package ‘ggplot2’ to generate all the graplis in

Transcribed image text: Use package ‘ggplot2’ to generate all the graplis in HW4. 1. Stock Prices: – Check out the yahoo webpage of historical stock price data for Netflix (NFLX): finance. yahoo.com/quote/NFL X/history? p=NFLX ). – Change the range of Date from 01/01/2021 to 09/30/2021. Click on “Apply” before “Download”….

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ggplot2 – Issues with layout in R Markdown

I’m taking over a project from another more experienced user of Rmd, the code ran for her but now that I’m trying, the following code is throwing this error: #Output the plot using plotly a<- plotly::ggplotly(cstr_volume_graph) %>% layout(legend = list( #this layout bit is to change position of legend, although…

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Simulated global warming affects endophytic bacterial and fungal communities of Antarctic pearlwort leaves and some bacterial isolates support plant growth at low temperatures

Sample collection Colobanthus quitensis samples were collected at King George Island near the Henryk Arctowski Polish Antarctic Station, Maritime Antarctica (62°14’ S, 58°48’ W) during the summer season (February 2018). Samples were collected inside the Antarctic Specially Protected Area (ASPA) 128 using permits provided by The Chilean Antarctic Institute (INACH)…

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Pyramind Plot using ggplot2 in R

So from the context of the plot, I am assuming that you don’t want to convert the values themselves, but rather convert the x-axis so that the male and female sides of the pyramid are mirrored? In which case, you can use abs. The function abs(x) computes the absolute value…

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R: How do you create a log-scale in ggplot2 using an arbitrary base?

I am producing a density plot with ggplot2 where I want to show the x values on a logarithmic scale. For a logarithm with base 10 the following code does the job: #Set parameters n <- 1000 logmu <- 6 logsd <- 10 #Generate values set.seed(1) VALUES <- exp(rnorm(n, mean…

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Multi-level cellular and functional annotation of single-cell transcriptomes using scPipeline

Software Figure preparation: CorelDRAW x8 (Corel); Bioinformatic analyses: R v 4.0.3 (R Foundation for Statistical Computing). Computational resources Analyses were run on a desktop computer with an Intel Core i9-10900L CPU (3.70 GHz, 10 cores, 20 threads) with 120 GB RAM running Windows 10 Pro (v21H2). Data preprocessing scRNA-seq data sets…

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Any way to get my curve plot that works in ggplot2 to work with Plotly’s ggplotly? dose-response curve – General

Since you are not providing a function, you need to provide a set of x and y points. For it to look smooth and be exact, you want to have many points. So something like this may do what you want: library(ggplot2) library(dr4pl) myresponse <- data.frame(“Dose”=c(16,8,4,2,1,0.5,0.25,0.125,0.062,0.031), “Response”=c(98.1,95.8,91.6,90.6,89.6,80,5,22,10,-10)) myresult <- dr4pl(myresponse,…

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ggplot2 – Adding horizontal title/label to bar charts in ggplot R

The default approach to achieve the kind of grouping would be via faceting, However, TBMK the default element_rect provided by ggplot2 does not offer the option to just draw a top line. One option would be to create a custom theme element to achieve that. To this end I adapted…

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ggplot2 – How can I create multiple plots from same dataset in R?

Let me first share a dummy data, from which I want to prepare ggplot graphs. library(tidyverse) set.seed(1) sample_size <- 1200 dates <- sample(seq(1,31),sample_size,replace = TRUE) Monthss <- sample(seq(1,12),sample_size,replace = TRUE) hrs <- sample(seq(1,23),sample_size,replace = TRUE) minutes <- sample(seq(1,59),sample_size,replace = TRUE) date_time_vector <- paste0(dates,”-“,Monthss,”-“,2022,” “,hrs,”:”,minutes) |> lubridate::parse_date_time(“dmy HM”) Conversion <- sample(c(TRUE,FALSE),sample_size,…

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r – How can I check/extract the range of any scale in ggplot (size, color, etc)

If I want to check what the range for the size scale is set to for the plot below, how can I do that in ggplot? plt <- ggplot(mpg, aes(displ, hwy, size = hwy)) + geom_point() + scale_size(range = c(0, 5)) plt For x and y I can use layer_scales(plt)$x$range$range…

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Comprehensive Analysis of NPSR1-AS1 as a Novel Diagnostic and Prognostic Biomarker Involved in Immune Infiltrates in Lung Adenocarcinoma

The incidence of lung adenocarcinoma (LUAD), the most common subtype of lung cancer, continues to make lung cancer the largest cause of cancer-related deaths worldwide. Long noncoding RNAs (lncRNAs) have been shown to have a significant role in both the onset and progression of lung cancer. In this study, we…

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Draw Table in Plot in R (4 Examples) | Barplot, Histogram & Heatmap – Stats Idea

  This article shows several alternatives on how to plot a table object in R programming. The article will consist of the following information: Here’s how to do it!   Creating Example Data Have a look at the example data below: x <- c(letters[1:4], letters[2:4], “d”) # Create example vector…

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Using with {ggplot2}

Using with {ggplot2} Install using: devtools::install_github(“nrennie/PrettyCols”) …

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Ggplot Save Plot With Code Examples

Ggplot Save Plot With Code Examples This article will demonstrate via examples how to resolve the Ggplot Save Plot error . ggsave(“filename.png”) We were able to fix the Ggplot Save Plot problem by looking at a number of different examples. How do I save a Ggplot plot? You can either…

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ggplot2 – Issue in creating polygon in ggplot in R

Why does my polygon look like two triangles instead of a box? Can some help explain how I can turn the polygon into a box? data <- structure(list(AREA = c(“a”, “a”, “b”, “b”), Lat = c(43.68389835, 43.68389835, 44.3395883, 44.3395883), Long = c(-88.22909367, -88.99888743, -88.22909367, -88.99888743)), row.names = c(NA, -4L), spec…

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Set Axis Breaks Of Ggplot2 Plot In R 3 Examples Specify Tick Marks Of Graph Scale X Con Code

Set Axis Limits in ggplot2 R Plot (3 Examples) | Adjust … 5 days ago Modification of Axis Limits with scale_x_continuous. We have basically two alternatives, if … Modification of Axis Limits with coord_cartesian. Another way to widen the axis ranges of … Cutting off Values with Zoom In. In…

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How to Create a GGPlot with Multiple Lines

Load ggplot2 package library(ggplot2) theme_set(theme_minimal()) Data head(economics) ## # A tibble: 6 x 6 ## date pce pop psavert uempmed unemploy ## <date> <dbl> <int> <dbl> <dbl> <int> ## 1 1967-07-01 507. 198712 12.5 4.5 2944 ## 2 1967-08-01 510. 198911 12.5 4.7 2945 ## 3 1967-09-01 516. 199113 11.7…

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r – Adding values as text in raster images – ggplot2

I am plotting values in SpeedClass as rasterfile. I want to add text to the each tile to show the AvgSpeed from column 3. enter image description here Here is my code so far: AllDataSBAvgSpeed <- aggregate(AllDataSB$speed ~ AllDataSB$milepost + AllDataSB$Time, data = AllDataSB, mean) colnames(AllDataSBAvgSpeed)[1] <- “milepost” colnames(AllDataSBAvgSpeed)[2] <-…

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ggplot2 – How to plot several outcomes for several groups in R ggplot?

I want to build a single graph displaying several outcomes (with different point- and lineshapes for each, respectively) for several strata (displayed in different colours) over time. Using this for one group works: data <- data.frame( time = rep(c(“Baseline”, “Follow-Up 1”, “Follow-Up 2”), each = 8), stratum = rep(c(“Intervention”, “Control”),…

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r – While running ggplot2 command, geom smooth is not working

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 giving a small portion of my task…

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Adding objects together in R (like ggplot layers)

I’m doing OOP R and was wondering how to make it so the + can be used to add custom objects together. The most common example of this I’ve found is in ggplot2 w/ adding geoms together. I read through the ggplot2 source code and found this github.com/hadley/ggplot2/blob/master/R/plot-construction.r It looks…

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The genus Serratia revisited by genomics

Merlino, C. P. Bartolomeo Bizio’s letter to the most eminent priest, Angelo Bellani, concerning the phenomenon of the red-colored polenta [translated from the Italian]. J. Bacteriol. 9, 527–543 (1924). Grimont, P. A. D. & Dulong de Rosnay, H. L. C. Numerical study of 60 strains of Serratia. J. Gen. Microbiol….

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Log2FC values slightly higher in some genes after DESeq2 shrinkage

Hi, I have a question about DESeq2 LFCshrinkage: Is it possible that some genes have a slightly higher LFC after shrinkage? It happened during my RNAseq DE analysis, I have very deeply sequenced samples with large base means. I tried visualizing using MAplot check, and it looks fine. I’m mainly…

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r – How can I change the order of stacking in ggplot2 stacked bar chart?

I’m trying to create a stacked bar chart, but I’ve run into an issue where ggplot2 automatically stacks the values in my chart based on magnitude rather than keeping the stack order the same between bars. Dataset: drive.google.com/file/d/1lriQafJRtGrNC6OD2FnHx9Rt-BT9ReVm/view?usp=sharing Code: library(viridis) library(ggplot2) ggplot(rank_df, aes(y = Rank, x = Kinase, fill =…

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Installation | _main.knit

Before you start the installation of R, make sure your computer software is up-to-date. To get the most out of R, it is usually best to update to the maximum possible operating system. On a Mac, under the  you can find About This Mac. Then, in the Overview Tab…

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What is the ggplot2 package in R?

Overview The programming language R is popular among statisticians and mathematicians for mathematical computations and programming. The language has many diverse libraries that help make a user’s programming journey easy. It also has built-in datasets that can be used for experimenting and learning. The ggplot2 is one of R’s most…

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ggplot2 – Query On geom_raster When Creating Maps

I have a code for creating a map that works. I am now trying to add a raster layer with salinity gradient. I have been following a couple of tutorials and my current approach goes as follows: # Loads .TIF file ~ Salinity <- stack(“Present.Surface.Salinity.Mean.tif”) # Converts .TIF into dataframe…

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graph – Force R to stop plotting abbreviated axis labels (scientific notation) – e.g. 1e+00

As a more general solution, you can use scales::format_format to remove the scientific notation. This also gives you lots of control around how exactly you want your labels to be displayed, as opposed to scales::comma which only does comma separations of the orders of magnitude. For example: require(ggplot2) require(scales) df…

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Live-seq enables temporal transcriptomic recording of single cells

Biological materials RAW264.7, 293T and HeLa cells were obtained from ATCC. RAW264.7 cells with Tnf-mCherry reporter and relA-GFP fusion protein (RAW-G9 clone) were kindly provided by I.D.C. Fraser (National Institutes of Health). The IBA cell line derived from the stromal vascular fraction of interscapular brown adipose tissue of young male…

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How to Change Number of Axis Ticks in ggplot2 (With Examples)

You can use the following basic syntax to change the number of axis ticks on plots in ggplot2: p + scale_x_continuous(n.breaks=10) + scale_y_continuous(n.breaks=10) The following example shows how to use this syntax in practice. Example: Change Number of Axis Ticks in ggplot2 Suppose we have the following data frame in…

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ggplot2 – Subsetting plots in R with pairs function

I have a simple question however I can’t find the answer. I have a dataset in R with 1000 rows and 5 columns as follows: data <- matrix(rnorm(1000 * 5, mean = 0, sd = 1), 1000, 5) colnames(data) <- c(“A”, “B”, “C”, “D”, “E”) I want to visually examine…

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How to Find Standard Deviation in R?

Being a statistical language, R offers standard function sd(’ ‘) to find the standard deviation of the values. So what is the standard deviation? ‘Standard deviation is the measure of the dispersion of the values’. The higher the standard deviation, the wider the spread of values. The lower the standard…

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Matplotlib Ggplot Style? The 6 Latest Answer

matplotlib style templates | matplotlib Tutorial matplotlib style templates | matplotlib Tutorial Images related to the topicmatplotlib style templates | matplotlib Tutorial Matplotlib Style Templates | Matplotlib Tutorial What happened to ggplot2? On 25 February 2014, Hadley Wickham formally announced that “ggplot2 is shifting to maintenance mode. This means that…

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Resolved: Is there a generalized version of scale_fill_distiller and scale_colour_distiller?

Question: I do different plots with ggplot2 and want them all to have the same colour. The thing is that I use different geoms that sometimes work with fill and sometimes with col. See here: df <- data.frame(x= 1:10, y= 1:10, col= c(1:5, 5:1)) library(ggplot2) gg1 <- ggplot(df, aes(x, group=…

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GGPLOT2 Question about formatting and arranging x-axis labels : rstats

I am new to using R; please be kind. PLOT 1: I have a dataset where I used Lubridate to mutate the hour-of-day, as a number, into a new column from out of a datetime column. When I first made the plot, the x-axis labels started at 0 and went…

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Bioconductor – HPiP

DOI: 10.18129/B9.bioc.HPiP     Host-Pathogen Interaction Prediction Bioconductor version: Release (3.15) HPiP (Host-Pathogen Interaction Prediction) uses an ensemble learning algorithm for prediction of host-pathogen protein-protein interactions (HP-PPIs) using structural and physicochemical descriptors computed from amino acid-composition of host and pathogen proteins.The proposed package can effectively address data shortages and data…

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How to Make Grouped Violinplot with jittered data points in R

In this post, we will learn how to make grouped violin plot with jittered data points on top of it using ggplot2 in R. One of the challenges in making grouped violin or box plots with jittered data points is proper alignment of data points and the underlying plot. In…

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Resolved: Adding a legend to ggplot

Question: I have the below dataset; Player Goals Shots Regan Charles-Cook 10 32 Tony Watt 9 36 Bruce Anderson 8 26 Liam Boyce 8 44 Kyogo Furuhashi 8 31 Alfredo Morelos 8 80 Christian Ramirez 8 41 Liel Abada 7 57 Martin Boyle 7 43 Kevin van Veen 7 45…

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Bioconductor – TrajectoryGeometry (development version)

DOI: 10.18129/B9.bioc.TrajectoryGeometry     This is the development version of TrajectoryGeometry; for the stable release version, see TrajectoryGeometry. This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns Bioconductor version: Development (3.16) Given a time series or pseudo-times series of gene expression data, we might wish to…

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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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