Visualization of RNA structure motifs
Salomon Marquez
2026-02-03
1 Load dataset
# Specify a working directory
directory <- "/Volumes/DataWinBackup/00_MASTER UOC BIOINFORMATICA - TEMPORAL/TFM-UOC/RNAstructure/rna-structure-prediction"
setwd(directory)
list.files() [1] "2D_structure_6overlapped_isoforms" "2D_structure_eocrc"
[3] "2D_structure_locrc" "6_isoforms.fasta"
[5] "bpRNA_st_stats_6_isoforms_all.csv" "bpRNA_st_stats_eocrc_all.csv"
[7] "bpRNA_st_stats_locrc_all.csv" "bpRNA_st_stats.py"
[9] "fasta_to_results_rnastructure.py" "figures"
[11] "isoforms_eocrc.fasta" "isoforms_locrc.fasta"
[13] "motifs_plots copy.Rmd" "motifs_plots_cache"
[15] "motifs_plots-copy_cache" "motifs_plots-copy.Rmd"
[17] "motifs_plots.html" "motifs_plots.Rmd"
[19] "README.md" "rnastructure_6_isoforms.csv"
[21] "rnastructure_eocrc.csv" "rnastructure_locrc.csv"
[23] "run_bpRNA.sh" # Read .csv file
bpRNA_6_isoforms <- read.csv("bpRNA_st_stats_6_isoforms_all.csv", header = TRUE,
row.names = 1, check.names = FALSE)
bpRNA_6_isoforms <- bpRNA_6_isoforms[7:12]
bpRNA_6_isoforms n_stems n_hairpins n_internal_loops n_bulges n_multiloops
ENST00000325327.4 5 2 1 2 0
ENST00000329305.6 5 1 4 0 0
ENST00000338983.7 7 2 3 2 0
ENST00000378292.9 6 2 1 3 0
ENST00000467155.7 6 1 3 2 0
ENST00000532465.1 5 2 3 0 0
n_external_regions
ENST00000325327.4 2
ENST00000329305.6 2
ENST00000338983.7 2
ENST00000378292.9 1
ENST00000467155.7 1
ENST00000532465.1 1# Read .csv file
bpRNA_eocrc <- read.csv("bpRNA_st_stats_eocrc_all.csv", header = TRUE, row.names = 1,
check.names = FALSE)
bpRNA_eocrc <- bpRNA_eocrc[7:12]
bpRNA_eocrc n_stems n_hairpins n_internal_loops n_bulges n_multiloops
ENST00000297268.11 7 1 5 1 0
ENST00000318426.6 3 1 2 0 0
ENST00000325327.4 5 2 1 2 0
ENST00000329305.6 5 1 4 0 0
ENST00000378292.9 6 2 1 3 0
ENST00000382040.4 7 2 2 3 0
ENST00000415602.5 5 4 0 0 1
ENST00000489749.1 4 1 2 1 0
n_external_regions
ENST00000297268.11 2
ENST00000318426.6 2
ENST00000325327.4 2
ENST00000329305.6 2
ENST00000378292.9 1
ENST00000382040.4 2
ENST00000415602.5 1
ENST00000489749.1 2
[ reached 'max' / getOption("max.print") -- omitted 2 rows ]# Read .csv file
bpRNA_locrc <- read.csv("bpRNA_st_stats_locrc_all.csv", header = TRUE, row.names = 1,
check.names = FALSE)
bpRNA_locrc <- bpRNA_locrc[7:12]
bpRNA_locrc n_stems n_hairpins n_internal_loops n_bulges n_multiloops
ENST00000263398.11 4 2 2 0 0
ENST00000316673.9 6 2 1 3 0
ENST00000319481.8 7 2 1 4 0
ENST00000338983.7 7 2 3 2 0
ENST00000374429.6 7 2 3 2 0
ENST00000378292.9 6 2 1 3 0
ENST00000637069.1 6 2 3 1 0
ENST00000642527.1 5 3 1 1 0
n_external_regions
ENST00000263398.11 1
ENST00000316673.9 1
ENST00000319481.8 1
ENST00000338983.7 2
ENST00000374429.6 2
ENST00000378292.9 1
ENST00000637069.1 2
ENST00000642527.1 1
[ reached 'max' / getOption("max.print") -- omitted 2 rows ]2 Data summary
# Summary of reports
summary(bpRNA_6_isoforms) n_stems n_hairpins n_internal_loops n_bulges n_multiloops
Min. :5.000 Min. :1.000 Min. :1.0 Min. :0.0 Min. :0
1st Qu.:5.000 1st Qu.:1.250 1st Qu.:1.5 1st Qu.:0.5 1st Qu.:0
Median :5.500 Median :2.000 Median :3.0 Median :2.0 Median :0
Mean :5.667 Mean :1.667 Mean :2.5 Mean :1.5 Mean :0
3rd Qu.:6.000 3rd Qu.:2.000 3rd Qu.:3.0 3rd Qu.:2.0 3rd Qu.:0
Max. :7.000 Max. :2.000 Max. :4.0 Max. :3.0 Max. :0
n_external_regions
Min. :1.0
1st Qu.:1.0
Median :1.5
Mean :1.5
3rd Qu.:2.0
Max. :2.0 summary(bpRNA_eocrc) n_stems n_hairpins n_internal_loops n_bulges n_multiloops
Min. :3.00 Min. :1.0 Min. :0.00 Min. :0.00 Min. :0.0
1st Qu.:4.25 1st Qu.:1.0 1st Qu.:1.00 1st Qu.:0.00 1st Qu.:0.0
Median :5.00 Median :2.0 Median :2.00 Median :0.50 Median :0.0
Mean :5.10 Mean :1.9 Mean :2.00 Mean :1.00 Mean :0.2
3rd Qu.:5.75 3rd Qu.:2.0 3rd Qu.:2.75 3rd Qu.:1.75 3rd Qu.:0.0
Max. :7.00 Max. :4.0 Max. :5.00 Max. :3.00 Max. :1.0
n_external_regions
Min. :1.00
1st Qu.:1.25
Median :2.00
Mean :1.70
3rd Qu.:2.00
Max. :2.00 summary(bpRNA_locrc) n_stems n_hairpins n_internal_loops n_bulges n_multiloops
Min. :4.0 Min. :1 Min. :1.0 Min. :0.0 Min. :0
1st Qu.:6.0 1st Qu.:2 1st Qu.:1.0 1st Qu.:1.0 1st Qu.:0
Median :6.0 Median :2 Median :2.5 Median :2.0 Median :0
Mean :6.1 Mean :2 Mean :2.2 Mean :1.9 Mean :0
3rd Qu.:7.0 3rd Qu.:2 3rd Qu.:3.0 3rd Qu.:3.0 3rd Qu.:0
Max. :7.0 Max. :3 Max. :4.0 Max. :4.0 Max. :0
n_external_regions
Min. :1.00
1st Qu.:1.00
Median :1.00
Mean :1.30
3rd Qu.:1.75
Max. :2.00 3 Motif visualization
# Heatmap plot of the 6 overlapped isoforms
bpRNA_6_isoforms_long <- bpRNA_6_isoforms |>
tibble::rownames_to_column("id") |>
pivot_longer(-id, names_to = "feature", values_to = "count")
ggplot(bpRNA_6_isoforms_long, aes(feature, id, fill = count)) + geom_tile(color = "white") +
scale_fill_viridis_c(option = "A") + theme_minimal() + theme(axis.text.x = element_text(angle = 45,
hjust = 1, vjust = 1), plot.title = element_text(hjust = 0.5) # center title
) +
labs(title = "Structural elements of overlapped isoforms", x = NULL, y = NULL,
fill = "Count")
# Heatmap plot of EOCRC transcripts
bpRNA_eocrc_long <- bpRNA_eocrc |>
tibble::rownames_to_column("id") |>
pivot_longer(-id, names_to = "feature", values_to = "count")
ggplot(bpRNA_eocrc_long, aes(feature, id, fill = count)) + geom_tile(color = "white") +
scale_fill_viridis_c(option = "A") + theme_minimal() + theme(axis.text.x = element_text(angle = 45,
hjust = 1, vjust = 1), plot.title = element_text(hjust = 0.5) # center title
) +
labs(title = "Structural elements of EOCRC top isoforms", x = NULL, y = NULL,
fill = "Count")
# Heatmap plot of LOCRC transcripts
bpRNA_locrc_long <- bpRNA_locrc |>
tibble::rownames_to_column("id") |>
pivot_longer(-id, names_to = "feature", values_to = "count")
ggplot(bpRNA_locrc_long, aes(feature, id, fill = count)) + geom_tile(color = "white") +
scale_fill_viridis_c(option = "A") + theme_minimal() + theme(axis.text.x = element_text(angle = 45,
hjust = 1, vjust = 1), plot.title = element_text(hjust = 0.5) # center title
) +
labs(title = "Structural elements of LOCRC top isoforms", x = NULL, y = NULL,
fill = "Count")
4 R Session Information
─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 4.5.1 (2025-06-13)
os macOS Ventura 13.7.3
system x86_64, darwin20
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/Madrid
date 2026-02-03
pandoc 3.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/x86_64/ (via rmarkdown)
quarto 1.5.57 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto
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