library(ggseqlogo)
SNI 截motif3的4-8位 E-value: 7.8e-016
prob_matrix <- matrix(c(
0.000000, 0.735709, 0.051225, 0.213066, # Position 4
0.242762, 0.634744, 0.000000, 0.122494, # Position 5
0.000000, 0.940609, 0.000000, 0.059391, # Position 6
0.998515, 0.000000, 0.000000, 0.001485, # Position 7
0.113586, 0.000742, 0.822569, 0.063103 # Position 8
), nrow = 5, byrow = TRUE) # 5 positions
# Transpose the matrix so rows are bases and columns are positions
prob_matrix <- t(prob_matrix)
# Set row names for the bases
rownames(prob_matrix) <- c("A", "C", "G", "T")
# Create the sequence logo
ggseqlogo(prob_matrix, seq_type = "DNA", col_scheme = "nucleotide2")
Sham 截motif3的4-8位 E-value: 2.8e-002
prob_matrix <- matrix(c(
0.326969, 0.000000, 0.673031, 0.000000, # Position 1
0.479714, 0.000000, 0.520286, 0.000000, # Position 2
0.205251, 0.436754, 0.357995, 0.000000, # Position 3
0.622912, 0.000000, 0.119332, 0.257757, # Position 4
0.000000, 0.000000, 1.000000, 0.000000 # Position 5
), nrow = 5, byrow = TRUE) # 5 positions
# Transpose the matrix so rows are bases and columns are positions
prob_matrix <- t(prob_matrix)
# Set row names for the bases
rownames(prob_matrix) <- c("A", "C", "G", "T")
ggseqlogo(prob_matrix, seq_type = "DNA", col_scheme = "nucleotide2")
sh 截motif3的2-6位 E-value: 1.1e-011
prob_matrix <- matrix(c(
0.000000, 0.936508, 0.000000, 0.063492, # Position 1
1.000000, 0.000000, 0.000000, 0.000000, # Position 2
0.000000, 0.000000, 1.000000, 0.000000, # Position 3
0.000000, 0.626984, 0.373016, 0.000000, # Position 4
0.000000, 0.904762, 0.000000, 0.095238 # Position 5
), nrow = 5, byrow = TRUE) # 5 positions
# Transpose the matrix so rows are bases and columns are positions
prob_matrix <- t(prob_matrix)
# Set row names for the bases
rownames(prob_matrix) <- c("A", "C", "G", "T")
# Print the matrix to verify
print(prob_matrix)
ggseqlogo(prob_matrix, seq_type = "DNA", col_scheme = "nucleotide2")
