Maximum bits in ggseqlogo is less then 2?
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Entering edit mode
9 days ago
Mattan ▴ 10

Hi all, I'm using this code as a toy example to see if I understand how ggseqlogo works

# Create a data frame with the sequences
sequences <- c("ACA","ATA","AGA","AAA","ATA","AGA")
df <- data.frame(Sequence = sequences)

# Plot the sequence logo
ggseqlogo(df$Sequence)

I fail to understand the results I'm getting. enter image description here

Why isn't the maximuum 2 bits for positions 0,2? Also, why is the middle poistion (1) isn't populated? We do know that G and T are more common there.

ggseqlogo • 303 views
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2
Entering edit mode
8 days ago
Mensur Dlakic ★ 27k

Most sequence logo implementations have a small sample correction by default. This is easy to test by using 15-20 sequences, in which case the height of terminal residues should be closer to 2 bits and the middle stack might show up. This is what I get after increasing the number of sequences to ~100.

enter image description here

You may need to turn the small sample correction off.

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2
Entering edit mode
8 days ago

The original paper describes the information at a position as:

Information(l) = 2 - (H(l) + e(n))

Here, Information(l) is the value along the y-axis in your plots. H(l) is the uncertainty at position l (which decreases when you have more of the same bases at that position in the sequence), while e(n) is a correction factor required when the number n of sample sequences is small. That correction factor is apparently described in this paper but it is also defined in the source code for ggseqlogo.

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Entering edit mode
8 days ago
bk11 ★ 2.7k

Did you check with method="prob" too?

ggseqlogo(df$Sequence, method="prob")

enter image description here

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