Editing Nanopore RNA Sequencing Protocol (section)

=====Plotting Results (ATF5)=====

Here we can plot the results for the ATF5 gene. This will be modified in a future iteration.

<code>R</code>
<syntaxhighlight lang="R">
suppressMessages (library(reshape2))
suppressMessages (library(ggplot2))
suppressMessages (library(ggrepel))
suppressMessages (library(tidyverse))
suppressMessages (library(stringr))

# Isolate ATF5
WT122021_nano_ATF5 <- subset(FAR91556_chr19_epinano_result, Start >= 49928403)
WT122021_nano_ATF5 <- subset(WT122021_nano_ATF5, End <= 49934438)
IDHMUT_nano_ATF5 <- subset(FAM95931_chr19_epinano_result, Start >= 49928403)
IDHMUT_nano_ATF5 <- subset(IDHMUT_nano_ATF5, End <= 49934438)
#WT_mod <- subset(WT122021_nano_ATF5, m6A_Prob >= 0.05)
#WT_unm <- subset(WT122021_nano_ATF5, m6A_Prob < 0.05)

# Note: Some of these data were generated view the MotifFinder script.
#49928702-49933935
# ATF5 Gene, Chr19:49929205-49933935
merge <- ggplot (WT122021_nano_ATF5) +
  ggtitle ("Merge") +
  # Underlying Strand
  geom_segment(aes(x=49928403, xend=49934438, y=0.125, yend=0.125), color="#383838", size=4) +
  # Exon 1 49,928,890 - 49,929,022
  geom_segment(aes(x=49928890, xend=49929022, y=0.125, yend=0.125), color="#858585", size=6) +
  # Exon 2 49,929,223 - 49,929,421
  geom_segment(aes(x=49929223, xend=49929421, y=0.125, yend=0.125), color="#858585", size=6) +
  # Exon 3 49,930,681 - 49,931,079
  geom_segment(aes(x=49930681, xend=49931079, y=0.125, yend=0.125), color="#858585", size=6) +
  # Exon 4 49,932,271 - 49,934,086
  geom_segment(aes(x=49932271, xend=49934086, y=0.125, yend=0.125), color="#858585", size=6) +
  # Location of RRACH sites in ATF5. This was ascertained using the Motif Finder function.
  #geom_linerange(data=ATF5_RRACH, aes(x=Hg38Position, ymin=0, ymax=1), color="#d9fbcb", size=0.4) +
  #geom_linerange(data=ATF5_MAZF, aes(x=Hg38Position, ymin=0, ymax=1), color="#476ad0", size=0.4) +
  # WT Dots
  geom_point(data=WT122021_nano_ATF5, aes(x=Start, y=m6A_Prob),shape = 21, colour = "black", fill = "#959595", size=2, stroke = 1.0) +
  # IDH Mut Dots
  geom_point(data=IDHMUT_nano_ATF5, aes(x=Start, y=m6A_Prob),shape = 21, colour = "black", fill = "#dd1818", size=2, stroke = 1.0) +
  # Instead of entering in the chromosome, paste it to the label from the data.
  xlab (paste0("Position on ", WT122021_nano_ATF5[1,1])) +
  ylab ("m6A Prob.") +
  theme_bw ()+
  theme (axis.text.x = element_text(face="bold", color="black",size=11),
         axis.text.y = element_text(face="bold", color="black", size=11),
         plot.title = element_text(color="black", size=24, face="bold.italic", hjust = 0.5),
         axis.title.x = element_text(color="black", size=15, face="bold"),
         axis.title.y = element_text(color="black", size=15, face="bold"),
         panel.background = element_blank(),
         legend.position = "none",
         axis.line = element_line(colour = "black", size=0.5))
#geom_text_repel (data=mod, aes(x=Position, y=ProbM, label=Position), color="red", box.padding=3, point.padding=3, segment.size  = 0.6, segment.color = "green")
</syntaxhighlight>

Final export on one graph:

<code>R</code>
<syntaxhighlight lang="R">
suppressMessages(library(gridExtra))
grid.arrange(wt, idh, merge, nrow = 2)
</syntaxhighlight>