Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Plotting DGE on R

    Good night!

    I'm trying to make a plot of my DGE through R from NOISeq + ComplexHeatmap packages.
    I have two dataframes, on the first i have the samples as columns and transcripts as rows. On the seocnd dataframe i have the DGE filtered by p, log2FC, means and theta value.

    I already make a plot with all my list, but i can' filter the data then plot only the differentially expressed genes.
    If i plot directly the DGE data.frame, he is following the colnames (log2fc, theta, prob and means), i want to use the filtered data and make a heatmap based on log to better visualize their pattern of expression.

    Here is how i proceed to plot all my data.frame
    mat = mynoiseq2[sample(nrow(mynoiseq.deg), nrow(mynoiseq.deg)), colnames(mynoiseq2)]
    hb = HeatmapAnnotation(barplot = anno_boxplot(mat2))
    hc = HeatmapAnnotation(barplot = anno_points(rnorm(10))
    mat_scaled = t(apply(mat, 1, scale))
    Heatmap(mat_scaled, col=rev(rainbow(10)), show_row_names=FALSE, show_column_names=TRUE, column_title_side="top",cluster_columns=FALSE, cluster_rows=FALSE, bottom_annotation = hb, top_annotation=hc, column_title="TSH")

    I just want to use the filtered data or filter and normalize.

Latest Articles

Collapse

  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM
  • seqadmin
    The Impact of AI in Genomic Medicine
    by seqadmin



    Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
    02-26-2024, 02:07 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 03-14-2024, 06:13 AM
0 responses
32 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-08-2024, 08:03 AM
0 responses
71 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-07-2024, 08:13 AM
0 responses
80 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-06-2024, 09:51 AM
0 responses
68 views
0 likes
Last Post seqadmin  
Working...
X