Tag: cnetplot

Home Bioconductor 3.17 Released April 26, 2023 Bioconductors: We are pleased to announce Bioconductor 3.17, consisting of 2230 software packages, 419 experiment data packages, 912 annotation packages, 27 workflows and 3 books. There are 79 new software packages, 7 new data experiment packages, no new annotation packages, 2 new workflows,…

Gene concept network plot by using GSEA SOFTWARE output on R 0 Hi Everyone! I am trying to plot a gene concept network with the output from GSEA SOFTWARE. I would like something as cnetplot function provided on R. I tried to plot the result, but it did not work…

Error in UseMethod(“rescale”) 0 @2528ae94 Last seen 17 hours ago United States While using cnetplot to plot enrichGo results, I am getting the following error. It used to work before, but now I am constantly getting this error. I am using clusterprofiler package gse <- enrichGO(gene = deGenes, ont =…

Hello, I’m working on creating a cnetplot based off of a compareCluster enrichment result. I want to plot 5 GO Biological Processes as the individual categories with the corresponding genes connecting with each one of them. I’m able to do this successfully with the cnetplot function, but since each category…

Hi All, I am trying to make cnet plots of differentially expressed genes between 2 tissue types, looking at specific pathways identified from enrichGO analysis. When I plot this a bunch of non-significantly regulated genes are appearing as uncolored dots and I am not sure how to stop this from…

I have a pathway plot using cnetplot() in R from the enrichplot package. I am able to change individual gene nodes’ colors no problem, but I want to change the beige pathway nodes colors and I can’t figure out how. I’ve tried different attempts from a github thread asking the…

Hi, Does not matter what I do, the legend saying “gene number” and “log2FC” overlaps all the time with the actual plot I tried different parameters of the cnetplot function and also tried to modify the plot after storing the plot to a variable but I do not find the…

cnetplot with enrichKEGG results 0 @5215d925 Last seen 11 hours ago Spain Hello! I’m trying to use cnetplot function with a KEGG enrichment object obtained from enrichKEGG function. However, I get the same error and I don’t know how to solve it. I’m using clusterProfiler package to perform this analysis….

Home Bioconductor 3.14 Released October 27, 2021 Bioconductors: We are pleased to announce Bioconductor 3.14, consisting of 2083 software packages, 408 experiment data packages, 904 annotation packages, 29 workflows and 8 books. There are 89 new software packages, 13 new data experiment packages, 10 new annotation packages, 1 new workflow,…

Can cnetplot plot points change shape in clusterprofiler? 0 I have a cnetplot and I am wondering if it is possible for me to do further categorising of the plot by point shape? I have a cnetplot of genes and their interacting pathways, but the genes also have a few…

cnetplot() : arguments to change color, node size and labels size not working 0 In cnetplot(), I am trying to use the arguments cex_category and cex_gene to change node size, cex_label_category and cex_label_gene to change labels size, and color_category and color_gene to change colors. However, none of these arguments seem…

I have a cnetplot from running enrichment with kegg using clusterprofiler. I have scores input as the fold change but for each gene in the plot they are not varying in colour to show their difference in the fold change score. My dataset is genes of entrez IDs and then…