Question: Modifications of graphs from Sleuth Object?
gravatar for BioBing
3.6 years ago by
BioBing130 wrote:

Dear Biostar users,

I have been using Kallisto/Sleuth to analyze my RNA-seq data and have a couple of questions related to the modification of heat maps based on a sleuth object (so), that I hope someone can help me with:

Question 1: I am a bit puzzled about what the "value" that goes from 0-6ish represents (see below) - what exactly does that mean? Is there a way to further modify the R-code below in order to get up- and down-regulation (minus - plus values) represented instead?

Question 2: How to modify the R-code further to add a dendrogram to the heatmap?

Thanks, Birgitte

The modified heat-map R-code:

plot_transcript_heatmap(so,Handling_type3$target_id,units = "tpm",trans = "log", offset = 1) +
scale_fill_gradient(low="white",high="steelblue", guide=guide_colorbar(direction="horizontal")) +
    axis.text.x = element_text(size=7),
    legend.position = "bottom",
    legend.text = element_text(size=7),
    legend.title = element_text(size=7))

The resulting plot:

The resulting plot

rna-seq R • 1.7k views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by BioBing130
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1294 users visited in the last hour