Question: Modifications of graphs from Sleuth Object?
0
gravatar for BioBing
19 months ago by
BioBing90
Denmark
BioBing90 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")) +
theme(axis.text.y=element_text(size=4),
    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 • 698 views
ADD COMMENTlink modified 19 months ago • written 19 months ago by BioBing90
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2005 users visited in the last hour