Tag: cnetplot

Preventing overlap of gene labels/names in cnetplot

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…

Continue Reading Preventing overlap of gene labels/names in cnetplot

Cnet plot showing non-significant genes within pathway

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…

Continue Reading Cnet plot showing non-significant genes within pathway

How to change pathway color nodes in cnetplot?

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…

Continue Reading How to change pathway color nodes in cnetplot?

cnetplot: How to control the size of the legend gene number and log2FC

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…

Continue Reading cnetplot: How to control the size of the legend gene number and log2FC

cnetplot with enrichKEGG results

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….

Continue Reading cnetplot with enrichKEGG results

Bioconductor – Bioconductor 3.14 Released

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,…

Continue Reading Bioconductor – Bioconductor 3.14 Released

Can cnetplot plot points change shape in clusterprofiler?

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…

Continue Reading Can cnetplot plot points change shape in clusterprofiler?

arguments to change color, node size and labels size not working

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…

Continue Reading arguments to change color, node size and labels size not working

How to colour points in cnetplot of clustprofiler?

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…

Continue Reading How to colour points in cnetplot of clustprofiler?