Modifications of graphs from Sleuth Object?
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Entering edit mode
5.9 years ago
BioBing ▴ 150

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

R RNA-Seq rna-seq • 2.5k views
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