SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
plotting 5 million points in R Jon17 Bioinformatics 10 01-19-2017 09:42 AM
Plotting in R aevgup Bioinformatics 6 04-29-2014 06:41 AM
edgeR plotting error stephenhart General 0 12-06-2012 03:07 AM
Plotting cuffdiff TCONS_### as glyphs Starr_Hazard Bioinformatics 0 04-25-2012 09:15 AM
tool for plotting bioenvisage General 1 02-15-2010 10:12 AM

Reply
 
Thread Tools
Old 09-16-2017, 05:37 PM   #1
luminasapientiae
Junior Member
 
Location: Brazil

Join Date: Sep 2017
Posts: 5
Exclamation 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.
luminasapientiae is offline   Reply With Quote
Reply

Tags
rna

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:30 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO