Tag: ComplexHeatmap

Hi, I’m attempting to separate the final column from the others (as shown in the plot below) due to the significantly greater number of barplots it contains compared to the rest. Could I possibly divide them and create distinct y-axis scales for each group? Any suggestion will be greatly appreciated!…

Mice The research conducted in this study complied with all of the relevant ethical regulations. The animal protocols were approved by and performed in accordance with the Institutional Animal Care and Use Committee of St. Jude Children’s Research Hospital. C57BL/6, OT-I50, pmel51 and Rosa26-Cas9 knock-in52 mice were purchased from The…

DOI: 10.18129/B9.bioc.TCGAbiolinks     TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data Bioconductor version: Release (3.5) The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses…

DOI: 10.18129/B9.bioc.maftools     Summarize, Analyze and Visualize MAF Files Bioconductor version: Release (3.6) Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal…

DOI: 10.18129/B9.bioc.SEtools     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SEtools. SEtools: tools for working with SummarizedExperiment Bioconductor version: 3.12 This includes a set of tools for working with the SummarizedExperiment class, including merging, melting, aggregation and plotting functions. In particular,…

DOI: 10.18129/B9.bioc.simona   Semantic Similarity in Bio-Ontologies Bioconductor version: Release (3.18) The package implements a rich set of methods for semantic similarity analysis on bio-ontologies. They include methods for information contents, similarities between two terms as well as similarities between two groups of terms. It also implements visualizations on DAGs….

Dear Fellows, I have reviewed the complex heatmap tutorial,but could not replicate it with my data. jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html Point is I am trying to annotate the heatmap from columns 1:5 (Group 1), 6:10 (Group 2), 11:15 (Group 3) up to group 5. my first attempt to generate heatmap worked: #complex heatmap…

Hi all, I’m trying to create a SPIA data file for all 483 xml files for the KEGG Orthology (KO) Database. I’m working with a non-model organism that is not supported by KEGG as it’s own organism, so I have to use the KEGG Orthology (KO) Database instead of a…

I’m trying to plot a heatmap of my RNA seq data there’s a 1847 rows containing the sample names at first row, the gene name at first column, other columns are the TPKM.But the multiple arguments keep occur when I want to selectively label a few genes. data <- read.csv(“forheatmapUPchipvenny.csv”,…

DOI: 10.18129/B9.bioc.nipalsMCIA   This is the development version of nipalsMCIA; to use it, please install the devel version of Bioconductor. Multiple Co-Inertia Analysis via the NIPALS Method Bioconductor version: Development (3.18) Computes Multiple Co-Inertia Analysis (MCIA), a dimensionality reduction (jDR) algorithm, for a multi-block dataset using a modification to the…

DOI: 10.18129/B9.bioc.TimeSeriesExperiment     Analysis for short time-series data Bioconductor version: Release (3.11) Visualization and analysis toolbox for short time course data which includes dimensionality reduction, clustering, two-sample differential expression testing and gene ranking techniques. The package also provides methods for retrieving enriched pathways. Author: Lan Huong Nguyen Maintainer: Lan…

Samples for H3K27ac ChIP–seq Samples were collected by the GTEx Consortium. The donor enrollment and consent, informed consent approval, histopathological review procedures, and biospecimen procurement methods and fixation were the same as previously described22. No compensation was provided to the families of participants. Massachusetts Institute of Technology Committee on the…

DOI: 10.18129/B9.bioc.blacksheepr   Outlier Analysis for pairwise differential comparison Bioconductor version: Release (3.17) Blacksheep is a tool designed for outlier analysis in the context of pairwise comparisons in an effort to find distinguishing characteristics from two groups. This tool was designed to be applied for biological applications such as phosphoproteomics…

DOI: 10.18129/B9.bioc.CeTF   Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis Bioconductor version: Release (3.17) This package provides the necessary functions for performing the Partial Correlation coefficient with Information Theory (PCIT) (Reverter and Chan 2008) and Regulatory Impact Factors (RIF) (Reverter et al….

DOI: 10.18129/B9.bioc.clustifyr   Classifier for Single-cell RNA-seq Using Cell Clusters Bioconductor version: Release (3.17) Package designed to aid in classifying cells from single-cell RNA sequencing data using external reference data (e.g., bulk RNA-seq, scRNA-seq, microarray, gene lists). A variety of correlation based methods and gene list enrichment methods are provided…

Hi, R studio server freezes and the .Rproj.user and .Rhistory files must be deleted to connect to an already running session. This behaviour is only resolved by uninstalling monocle3 and comes back when I re-install monocle3. I tried the development and beta branch of Monocle3. I had the same issue…

I want to see the circular heatmap in the output of my code in R Shiny App. However, when I first run the code, circular heatmap works fine, but no longer outputs circular. library(shiny) library(shinydashboard) library(ComplexHeatmap) library(BiocManager) library(circlize) library(RColorBrewer) # Shiny app ui <- dashboardPage( dashboardHeader(title = “Circular Heatmap”), dashboardSidebar(),…

I’ve been making various heatmaps for different gene sets and I added the log2FoldChange values as an extra column, but I need to leave it as a barplot, but I’ve been lost on how to put those log2FoldChange values to appear as bars. Any help is appreciated, thanks 😉 “`r…

How can I sort the Circular heatmap labels in alphabetical order? The codes where I created the circular in my code are as follows: tmp4 <- tmp4[order(row.names(tmp4)), ] tmp5 <- tmp5[order(row.names(tmp5)), ] write.csv(tmp5, “circos_control_data_min.csv”) rownames(datab) <- datab$Metabolite_ID datab2 <- datab[rownames(tmp4), ] # datab2 <- datab[datab$Metabolite_ID %in% rownames(tmp4), ] # datab2…

R Heatmap A short tutorial for decent heat maps in R 图片 How to Create a Beautiful Interactive Heatmap in R – Datanovia 图片 Heatmap in R: Static and Interactive Visualization – Datanovia 图片 A short tutorial for decent heat maps in R 图片 How To Make a Heatmap in…

Hello all, I have plotted an oncoprint following this link but i am facing trouble in arranging the labels and modifying annotations, here is the code i have used. Input: Sample1 Sample2 Sample3 Sample4 Sample5 Gene1 “” “Nonsense” “” “” “Nonsense” “Nonsense” Gene2 “” “” “” “” “” “” Gene3…

Heatmap for ATAC-seq 0 Hi all, I apply similar code that I used for RNA-seq (DeSeq2) to ATAC-seq to make a heatmap, so I am not use if it still makes sense. The function here is Heatmap(), not pheatmap(). Instead of count matrix for genes, here I use consensus_peaks.mLb.clN.featureCounts.txt, a…

Primers, plasmids, bacterial strains, and growth conditions Primers, plasmids, and strains used in this study are listed in Tables S1–S3, respectively. Escherichia coli strains MG1655, DH10B, MDS42, and their derivates were cultured in LB medium at 37 °C, with shaking at 220 rpm. All the recombinants containing the temperature-sensitive pSC101-derived plasmid were cultured…

DOI: 10.18129/B9.bioc.CATALYST     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see CATALYST. Cytometry dATa anALYSis Tools Bioconductor version: 3.12 Mass cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing…

Isolate storage, growth, and identification Historical BFG isolates originally cultured from clinical material between 1973 and 2018 were stored either lyophilized or frozen in skim milk media at the National Institutes of Health Clinical Center Department of Laboratory Medicine (Bethesda, MD). Isolates were de-identified and metadata including year and source/site…

I have a shiny app the I’ve been publishing to a Posit Connect server hosted by the HPC at my institution. The app is from my RStudio on my laptop . The Cluster has configured Posit Connect to use Package Manager to host and vet packages for security and stability….

complex heatmap with CPM 0 Hi all, To draw complex heatmap, I started to use ComplexHeatmap package in R. I have a RNASeq data which has 2 cell lines with 2 conditions (CellLine1-WT, CellLine1-KO, CellLine2-WT, CellLine2-KO). When I try to draw heatmap with log2(CPM+1) values, the h2052 doesnt cluster together…

List of congruent tip TEC markers The list of congruent tip TEC markers was extracted from a publicly available lung tumor study8. In brief, to identify congruent tip cell markers across freshly isolated human and murine TECs, as well as cultured human TECs, all genes that were most highly expressed…

How to add annotation columns with specific colors to the heatmap? 0 Hello, I wanted to create a heatmap with 4-5 annotation columns, the point is these annotations might have values 0 or 1 , like the uploaded image each column should have different color to the other. for example…

Is it possible to add a dendrogram as a top annotation using ComplexHeatmap ? 0 I want to had a custom dendrogram to an heatmap. I know i can add like this: dend = as.dendrogram(hclust(dist(gene_matrix), method = ‘ward.D’)) dend = color_branches(dend, k = 4) Heatmap(gene_matrix, name = “Altered”,top_annotation= colAnn, cluster_columns…

How to keep ComplexHeatmap from reordering annotations 0 I am using complex heatmap to plot a gene alteration matrix with a dendrogram on top but, below the dendrogram I want to have a color map with the diseases that each patient has: column_ha = HeatmapAnnotation(Disease = Clinical_data$Disease ) Heatmap(t(gene_matrix), name…

Hi everyone First of all thank you for making rna-seq data much more accessible to an average clinical doctor through the DEseq2 packages and vignettes. I am though running into some trouble: I have a dataset of Nanostring mRNA-data from clinical study, which later was followed up. I therefore have…

Sign up for my newsletter to not miss a post like this divingintogeneticsandgenomics.ck.page/newsletter The problem Let me be clear, when you have gazillions of data points in a scatter plot, you want to deal with the overplotting to avoid drawing misleading conclusions. Let’s start with a single-cell example. Load the…

DOI: 10.18129/B9.bioc.MatrixQCvis     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see MatrixQCvis. Shiny-based interactive data-quality exploration for omics data Bioconductor version: 3.13 Data quality assessment is an integral part of preparatory data analysis to ensure sound biological information retrieval. We present here…

Hello all, I have been plotting a heatmap through ComplexHeatmap, everything is fine but when trying to map color to some levels, I got an error. Here is the code, I used h.col.study <- HeatmapAnnotation( Study=meta %>% arrange(match(Sample, colnames(hm.data))) %>% filter(Sample %in% colnames(hm.data)) %>% pull(Study), Soil_origin=meta %>% arrange(match(Sample, colnames(hm.data))) %>%…

How to show only highly clustered genes in a heatmap, and the rest will hide 1 Hello all, I have done the correlation analysis between the genes at a particular condition and now am trying to plot a heatmap through complexheatmap, but the problem is that i have 270 genes…

Samples used in this observational cohort study (tumor tissue and matched healthy colon tissue, AC-ICAM cohort) are from patients with colon cancer diagnosed at Leiden University Medical Center, the Netherlands, from 2001 to 2015 that did not object for future use of human tissues for scientific research and that were…

Error in colorRamp2(c(quantile(mean)[1], quantile(mean)[4], c(“white”, : argument “colors” is missing, with no default 0 col_AveExpr <- colorRamp2(c(quantile(mean)[1], quantile(mean)[4], c(“white”, “black”))) Error in colorRamp2(c(quantile(mean)[1], quantile(mean)[4], c(“white”, : argument “colors” is missing, with no default I am trying to make heatmap from sigs.df using complex heatmap, while making color code for average…

Overlapping on side of heatmap 0 Hi everyone, I constructed the heatmap below to display the results of my differential expression analysis through the Heatmap function from the ComplexHeatmap package. On the right side, the gene symbol seems to be overlapping with the number. How can this be fixed, I…

DOI: 10.18129/B9.bioc.mastR   Markers Automated Screening Tool in R Bioconductor version: Release (3.17) mastR is an R package designed for automated screening of signatures of interest for specific research questions. The package is developed for generating refined lists of signature genes from multiple group comparisons based on the results from…

Closed. This question needs debugging details. It is not currently accepting answers. This post was edited and submitted for review 2 hours ago. I have the following data: I have to plot a heatmap as below with “Person”, “sex” as x-axis annotations at the top…

Hi, I created heatmap with complexheatmap package. I tried to replace the annotation name position of “adj_P” from bottom to top by annotation_names_side function, but still “adj_P” is at bottom by following script. How should I fix it? Thanks in advance. left_ha = rowAnnotation(adj_P = anno_barplot(df_heat_1$negative_log10_of_adjusted_p_value, axis_param = list(side =…

color key heatmap 0 Hi there, I have a generated this heatmap using complexheatmap function but i was unable to insert the color key intensity in it.Can someone help me who had the same problem? My command is: heatmap(mat,cluster_rows = T, cluster_columns = F,column_lables=colnames(mat), main = “Differentially expressed genes of…

heatmap color key 0 Hi there, I have a generated this heatmap using complexheatmap function but i was unable to insert the color key intensity in it.and i wanted to change the color of the heatmap.Can someone help me who had the same problem? My command is: heatmap(mat,cluster_rows = T,…

This is the development version of GenomicRanges; for the stable release version, see GenomicRanges. The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing…

Deseq2/ComplexHeatmap – is it possible to combine 4 heatmaps together? 0 I am working on a project that studies how gene expression may change across generations with repeated treatment. I have 5 generations that I’m looking at and each generation consists of 3 biological replicates for the control and the…

How to Remove Sample Names from Heatmap 1 Hi there, I constructed a heatmap to display the results of my differential expression analysis through the Heatmap function from the ComplexHeatmap package. As I have many samples (400+) the sample names are unreadable and therefore I would just like to remove…

I am working DESeq2 i wanted i proper boxplot but i don’t understand what wrong i am doing and i wanted to know how to properly plot the x and y axis what parameters should be taken for boxplot . here’s my code: library(“DESeq2”) library(“ggplot2”) counts<-read.delim(“PC_1.csv”,header = TRUE, row.names =…

Tool:PyComplexHeatmap: a Python package to visualize multimodal genomics data 0 PyComplexHeatmap is a Python package to plot complex heatmap (cluster map). We present PyComplexHeatmap, an all-inclusive Python library for heatmap visualization, inspired by the ComplexHeatmap package currently available in R. PyComplexHeatmap is built upon the matplotlib library and features a…

How to extract proteins from PCs in plot_pca in DEP package? 1 I am using DEP package to analyze proteomics data. I did PCA for my samples (see the following plot) and wish to extract proteins in PC1 for further analysis. However, the objects x and y generated by the…

I have a dataset with following format. X M1. M2. … new_cell_type cac1. 1.5 1 … T cac2. 1.4 1.4 … M cac3. 0.5 1.1 … T cac4. 0.1 1 … N I want to plot a heatmap based on the above data where rows of the heatmap as cells…

DOI: 10.18129/B9.bioc.iSEE     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see iSEE. Interactive SummarizedExperiment Explorer Bioconductor version: 3.14 Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of…

Hi, I was working on marking genes of interest on the heatmap via ComplexHeatmap R package. Instead of specifying row numbers in anno_mark function, I specified a vector of genes to mark on the heatmap (see below) and used a combination of which() and %in% to isolate the row indices…

How to compare RNA expression correlation? 1 I have a set of genes that is important for the cell cycle and DNA damage. I wish to compare the RNA expression of these genes between each two cell lines and generate a heatmap to visualize the correlation (the x and y…

DOI: 10.18129/B9.bioc.HilbertCurve     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see HilbertCurve. Making 2D Hilbert Curve Bioconductor version: 3.13 Hilbert curve is a type of space-filling curves that fold one dimensional axis into a two dimensional space, but with still preserves the…

DOI: 10.18129/B9.bioc.PathoStat     PathoStat Statistical Microbiome Analysis Package Bioconductor version: Release (3.11) The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts,…

Cell culture IMR90 (CCL-186) and WI38 (AG06814-N) fibroblasts were purchased from ATCC and the Coriell Institute for Medical Research, respectively. IMR90 and WI38 fibroblasts were grown under 7.5% CO2 and 3% O2 in GlutaMax-DMEM (Gibco, 10569-010) supplemented with 0.1 mM non-essential amino acids (Corning, 25-025-Cl) and 15% fetal bovine serum (VWR/Seradigm,…

DOI: 10.18129/B9.bioc.ComplexHeatmap     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see ComplexHeatmap. Make Complex Heatmaps Bioconductor version: 3.14 Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly…

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,…

DOI: 10.18129/B9.bioc.cytoKernel     Differential expression using kernel-based score test Bioconductor version: Release (3.14) cytoKernel implements a kernel-based score test to identify differentially expressed features in high-dimensional biological experiments. This approach can be applied across many different high-dimensional biological data including gene expression data and dimensionally reduced cytometry-based marker expression…

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…

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…

1. Oh, J. et al. Biogeography and individuality shape function in the human skin metagenome. Nature 514, 59–64 (2014). 2. Byrd, A. L., Belkaid, Y. & Segre, J. A. The human skin microbiome. Nat. Rev. Microbiol. 16, 143–155 (2018). CAS  PubMed  Google Scholar  3. Oh, J. et al. Temporal stability…

DOI: 10.18129/B9.bioc.monaLisa     Binned Motif Enrichment Analysis and Visualization Bioconductor version: Release (3.14) Useful functions to work with sequence motifs in the analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility…

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…

Tutorial:A simple tutorial for a complex ComplexHeatmap 0 This is being added in response to my message on Twitter and LinkedIn about ComplexHeatmap. The new message is here. Many folks seemed interested in understanding how such figures could be made; so, I have decided to make the rheumatoid arthritis gene…

CeTF is an C/C++ implementation in R for PCIT [6] and RIF [7] algorithms, which initially were made in FORTRAN language. From these two algorithms, it was possible to integrate them in order to increase performance and Results. Input data may come from microarray, RNA-seq, or single-cell RNA-seq. The input…

R Programming – how to make a simple heat map 5 Hi can anyone guide me how to make a simple heat map in R? Heatmap R • 264 views There is github.com/XiaoLuo-boy/ggheatmap which is fully ggplot in case you feel more comfortable with it rather than the suggested pheatmap/ComplexHeatmap…

R Programming 4 Hi can anyone guide me how to make a simple heat map in R? in Heatmap R • 201 views There is github.com/XiaoLuo-boy/ggheatmap which is fully ggplot in case you feel more comfortable with it rather than the suggested pheatmap/ComplexHeatmap packages and want to have a consistent…