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Update docs from Malachi poster

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gatoravi committed Apr 22, 2016
1 parent 4f0e589 commit f1a20fac2b9948c887451f65849226dc5956e4d5
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@@ -2,3 +2,6 @@ build/
site/
.*.swp
*pyc
*.pdf
*Rdata
*Rhistory
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BIN +37.5 KB (120%) docs/images/anchor_examples.png
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BIN -16.4 KB (90%) docs/images/csei_examples.png
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@@ -3,12 +3,12 @@
library(ggplot2)
library(grid)
p <- ggplot() + ylim(-10, 110) + xlim(-10, 200) + theme(axis.text = element_blank()) + xlab("") + ylab("")+ theme(axis.ticks = element_blank()) + ggtitle("Anchor-annotation examples")
p <- ggplot() + ylim(-10, 110) + xlim(-20, 220) + theme_classic() + theme(axis.line=element_blank(), axis.text = element_blank()) + xlab("") + ylab("")+ theme(axis.ticks = element_blank()) + ggtitle("")
#Topmost transcript
p <- p + geom_rect(aes(xmin = 10, ymin = 90, xmax = 30, ymax = 100)) + geom_rect(aes(xmin = 40, ymin = 90, xmax = 60, ymax = 100)) + geom_rect(aes(xmin = 70, ymin = 90, xmax = 90, ymax = 100)) + geom_rect(aes(xmin = 100, ymin = 90, xmax = 120, ymax = 100)) + geom_rect(aes(xmin = 130, ymin = 90, xmax = 150, ymax = 100)) + geom_segment(aes(x = 30, y = 95, xend = 40, yend = 95), arrow = arrow(length = unit(0.5, "cm"))) + geom_segment(aes(x = 60, y = 95, xend = 70, yend = 95), arrow = arrow(length = unit(0.5, "cm")))+ geom_segment(aes(x = 90, y = 95, xend = 100, yend = 95), arrow = arrow(length = unit(0.5, "cm")))+ geom_segment(aes(x = 120, y = 95, xend = 130, yend = 95), arrow = arrow(length = unit(0.5, "cm")))
p <- p + geom_rect(aes(xmin = -10, xmax = 10, ymin = 70, ymax = 80)) + geom_rect(aes(xmin = 70, xmax = 90, ymin = 70, ymax = 80)) + geom_rect(aes(xmin = 100, ymin = 70, xmax = 120, ymax = 80)) + geom_rect(aes(xmin = 130, ymin = 70, xmax = 150, ymax = 80)) + geom_segment(aes(x = 10, xend = 70, y = 75, yend = 75), arrow = arrow(length = unit(0.5, "cm"))) + geom_segment(aes(x = 90, y = 75, xend = 100, yend = 75), arrow = arrow(length = unit(0.5, "cm"))) + geom_segment(aes(x = 120, y = 75, xend = 130, yend = 75), arrow = arrow(length = unit(0.5, "cm")))
p <- p + geom_rect(aes(xmin = 10, ymin = 50, xmax = 30, ymax = 60)) + geom_rect(aes(xmin = 100, ymin = 50, xmax = 120, ymax = 60)) + geom_rect(aes(xmin = 130, ymin = 50, xmax = 150, ymax = 60)) + geom_segment(aes(x = 30, y = 55, xend = 100, yend = 55), arrow = arrow(length = unit(0.5, "cm"))) + geom_segment(aes(x = 120, y = 55, xend = 130, yend = 55), arrow = arrow(length = unit(0.5, "cm")))
p <- p + geom_rect(fill = "#3363CC", aes(xmin = 0, ymin = 92.5, xmax = 10, ymax = 97.5)) + geom_rect(fill = "#3363CC", aes(xmin = 10, ymin = 90, xmax = 30, ymax = 100)) + geom_rect(fill = "#3363CC", aes(xmin = 40, ymin = 90, xmax = 60, ymax = 100)) + geom_rect(fill = "#3363CC", aes(xmin = 70, ymin = 90, xmax = 90, ymax = 100)) + geom_rect(fill = "#3363CC", aes(xmin = 100, ymin = 90, xmax = 120, ymax = 100)) + geom_rect(fill = "#3363CC", aes(xmin = 130, ymin = 90, xmax = 150, ymax = 100)) + geom_rect(fill = "#3363CC", aes(xmin = 150, ymin = 92.5, xmax = 160, ymax = 97.5)) + geom_segment(aes(x = 30, y = 95, xend = 40, yend = 95), arrow = arrow(length = unit(0.5, "cm"))) + geom_segment(aes(x = 60, y = 95, xend = 70, yend = 95), arrow = arrow(length = unit(0.5, "cm")))+ geom_segment(aes(x = 90, y = 95, xend = 100, yend = 95), arrow = arrow(length = unit(0.5, "cm")))+ geom_segment(aes(x = 120, y = 95, xend = 130, yend = 95), arrow = arrow(length = unit(0.5, "cm")))
p <- p + geom_rect(fill = "#3363CC", aes(xmin = -20, ymin = 72.5, xmax = -10, ymax = 77.5)) + geom_rect(fill = "#3363CC", aes(xmin = -10, xmax = 10, ymin = 70, ymax = 80)) + geom_rect(fill = "#3363CC", aes(xmin = 70, xmax = 90, ymin = 70, ymax = 80)) + geom_rect(fill = "#3363CC", aes(xmin = 100, ymin = 70, xmax = 120, ymax = 80)) + geom_rect(fill = "#3363CC", aes(xmin = 130, ymin = 70, xmax = 150, ymax = 80)) + geom_rect(fill = "#3363CC", aes(xmin = 150, ymin = 72.5, xmax = 160, ymax = 77.5)) + geom_segment(aes(x = 10, xend = 70, y = 75, yend = 75), arrow = arrow(length = unit(0.5, "cm"))) + geom_segment(aes(x = 90, y = 75, xend = 100, yend = 75), arrow = arrow(length = unit(0.5, "cm"))) + geom_segment(aes(x = 120, y = 75, xend = 130, yend = 75), arrow = arrow(length = unit(0.5, "cm")))
p <- p + geom_rect(fill = "#3363CC", aes(xmin = 0, ymin = 52.5, xmax = 10, ymax = 57.5)) + geom_rect(fill = "#3363CC", aes(xmin = 10, ymin = 50, xmax = 30, ymax = 60)) + geom_rect(fill = "#3363CC", aes(xmin = 100, ymin = 50, xmax = 120, ymax = 60)) + geom_rect(fill = "#3363CC", aes(xmin = 130, ymin = 50, xmax = 150, ymax = 60)) + geom_rect(fill = "#3363CC", aes(xmin = 150, ymin = 52.5, xmax = 160, ymax = 57.5)) + geom_segment(aes(x = 30, y = 55, xend = 100, yend = 55), arrow = arrow(length = unit(0.5, "cm"))) + geom_segment(aes(x = 120, y = 55, xend = 130, yend = 55), arrow = arrow(length = unit(0.5, "cm")))
#Plot junctions
p <- p + geom_rect(aes(xmin = 20, ymin = 30, xmax = 30, ymax = 35), fill = "red") + geom_rect(aes(xmin = 40, ymin = 30, xmax = 50, ymax = 35), fill = "red") + geom_segment(aes(x = 30, y = 32.5, xend = 40, yend = 32.5), arrow = arrow(length = unit(0.5, "cm")))
@@ -20,16 +20,17 @@ p <- p + geom_rect(aes(xmin = -5, ymin = -10, xmax = 5, ymax = -5), fill = "red"
#Add labels
p <- p + annotate("text", label = "Transcripts", x = 7, y = 105, size = 5)
p <- p + annotate("text", label = "Junctions", x = 5, y = 42.5, size = 5)
p <- p + annotate("text", label = "DA", x = 90, y = 32.5, size = 5)
p <- p + annotate("text", label = "NDA", x = 90, y = 22.5, size = 5)
p <- p + annotate("text", label = "D", x = 90, y = 12.5, size = 5)
p <- p + annotate("text", label = "A", x = 90, y = 2.5, size = 5)
p <- p + annotate("text", label = "N", x = 90, y = -7.5, size = 5)
p <- p + annotate("text", label = "Annotations from regtools", x = 120, y = 42.5, size = 5)
p <- p + annotate("text", label = "'DA': Known donor-acceptor", x = 140, y = 32.5, size = 5)
p <- p + annotate("text", label = "'NDA': Novel donor-acceptor combination", x = 140, y = 22.5, size = 5)
p <- p + annotate("text", label = "'D': Novel donor", x = 90, y = 12.5, size = 5)
p <- p + annotate("text", label = "'A': Novel acceptor", x = 90, y = 2.5, size = 5)
p <- p + annotate("text", label = "'N': Novel acceptor and novel donor.", x = 90, y = -7.5, size = 5)
#Add lines to make it clear
p <- p + geom_vline(xintercept = 30, linetype = "longdash") + geom_vline(xintercept = 40, linetype = "longdash") + geom_vline(xintercept = 70, linetype = "longdash")
print(p)
ggsave("anchor_examples.png")
ggsave("anchor_examples.pdf")
@@ -7,21 +7,26 @@ library(grid)
wrapper <- function(x, ...) paste(strwrap(x, ...), collapse = "\n")
#Setup plot skeleton
p <- ggplot() + ylim(50, 110) + theme(axis.text = element_blank()) + xlab("") + ylab("") + theme(axis.ticks = element_blank()) + ggtitle("'cis-splice-effects identify' examples")
p <- ggplot() + ylim(50, 110) + theme_classic() + theme(axis.line=element_blank(), axis.text = element_blank()) + xlab("") + ylab("") + theme(axis.ticks = element_blank()) + ggtitle("")
#Topmost transcript
p <- p + geom_rect(aes(xmin = 10, ymin = 90, xmax = 30, ymax = 100)) + geom_rect(aes(xmin = 40, ymin = 90, xmax = 60, ymax = 100)) + geom_rect(aes(xmin = 70, ymin = 90, xmax = 90, ymax = 100)) + geom_rect(aes(xmin = 100, ymin = 90, xmax = 120, ymax = 100)) + geom_rect(aes(xmin = 130, ymin = 90, xmax = 150, ymax = 100)) + geom_segment(aes(x = 30, y = 95, xend = 40, yend = 95), arrow = arrow(length = unit(0.5, "cm"))) + geom_segment(aes(x = 60, y = 95, xend = 70, yend = 95), arrow = arrow(length = unit(0.5, "cm")))+ geom_segment(aes(x = 90, y = 95, xend = 100, yend = 95), arrow = arrow(length = unit(0.5, "cm")))+ geom_segment(aes(x = 120, y = 95, xend = 130, yend = 95), arrow = arrow(length = unit(0.5, "cm")))
p <- p + geom_rect(fill = "#3363CC", aes(xmin = 5, ymin = 92.5, xmax = 10, ymax = 97.5)) + geom_rect(fill = "#3363CC", aes(xmin = 10, ymin = 90, xmax = 30, ymax = 100)) + geom_rect(fill = "#3363CC", aes(xmin = 40, ymin = 90, xmax = 60, ymax = 100)) + geom_rect(fill = "#3363CC", aes(xmin = 70, ymin = 90, xmax = 90, ymax = 100)) + geom_rect(fill = "#3363CC", aes(xmin = 100, ymin = 90, xmax = 120, ymax = 100)) + geom_rect(fill = "#3363CC", aes(xmin = 130, ymin = 90, xmax = 150, ymax = 100)) + geom_rect(fill = "#3363CC", aes(xmin = 150, ymin = 92.5, xmax = 155, ymax = 97.5)) + geom_segment(aes(x = 30, y = 95, xend = 40, yend = 95), arrow = arrow(length = unit(0.5, "cm"))) + geom_segment(aes(x = 60, y = 95, xend = 70, yend = 95), arrow = arrow(length = unit(0.5, "cm")))+ geom_segment(aes(x = 90, y = 95, xend = 100, yend = 95), arrow = arrow(length = unit(0.5, "cm")))+ geom_segment(aes(x = 120, y = 95, xend = 130, yend = 95), arrow = arrow(length = unit(0.5, "cm")))
#Plot variants
p <- p + geom_rect(aes(xmin = 28, ymin = 74, xmax = 30, ymax = 79))
p <- p + geom_rect(fill = "#006600", aes(xmin = 28, ymin = 74, xmax = 30, ymax = 79))
#Plot junctions
p <- p + geom_rect(aes(xmin = 20, ymin = 55, xmax = 30, ymax = 59), fill = "red") + geom_rect(aes(xmin = 70, ymin = 55, xmax = 80, ymax = 59), fill = "red") + geom_segment(aes(x = 30, y = 57, xend = 70, yend = 57), arrow = arrow(length = unit(0.5, "cm")))
#Plot dotted vertical lines
p <- p + geom_vline(xintercept = 30, linetype = "longdash") + geom_vline(xintercept = 70, linetype = "longdash")
#Add labels
p <- p + annotate("text", label = "Transcript annotation in the GTF file", x = 45, y = 105, size = 5)
p <- p + annotate("text", label = "Variant called in the genomic data", x = 45, xmin = 10, y = 85, size = 5)
p <- p + annotate("text", label = "Spliced junction identified by regtools from the RNAseq alignments", x = 78, y = 65, size = 5)
p <- p + annotate("text", label = "Transcript annotation", x = 120, y = 105, size = 5)
p <- p + annotate("text", label = "Variant called in the genomic data", x = 120, xmin = 10, y = 85, size = 5)
p <- p + annotate("text", label = "Spliced junction identified by regtools", x = 120, y = 65, size = 5)
print(p)
ggsave("csei_examples.png")
ggsave("csei_examples.pdf")
@@ -7,27 +7,29 @@ library(grid)
wrapper <- function(x, ...) paste(strwrap(x, ...), collapse = "\n")
#Setup plot skeleton
p <- ggplot() + ylim(30, 55) + theme(axis.text = element_blank()) + xlab("") + ylab("")+ theme(axis.ticks = element_blank()) + scale_x_continuous(breaks=-10:70) + ggtitle("Variant annotation")
p <- ggplot() + ylim(30, 50) + theme_classic() + theme(axis.line=element_blank(), axis.text = element_blank()) + xlab("") + ylab("")+ theme(axis.ticks = element_blank()) + scale_x_continuous(breaks=-10:70) + ggtitle("")
#Topmost transcript
p <- p + geom_rect(aes(xmin = 10, ymin = 40, xmax = 30, ymax = 50)) + geom_rect(aes(xmin = 40, ymin = 40, xmax = 60, ymax = 50)) + geom_segment(aes(x = 30, y = 45, xend = 40, yend = 45), arrow = arrow(length = unit(0.5, "cm")))
p <- p + geom_rect(fill = "#3363CC", aes(xmin = 10, ymin = 40, xmax = 30, ymax = 45)) + geom_rect(fill = "#3363CC", aes(xmin = 40, ymin = 40, xmax = 60, ymax = 45)) + geom_segment(aes(x = 30, y = 42.5, xend = 40, yend = 42.5), arrow = arrow(length = unit(0.5, "cm")))
#Plot variants
p <- p + geom_rect(aes(xmin = 22, ymin = 34, xmax = 23, ymax = 35), fill = "red")
p <- p + geom_rect(aes(xmin = 27, ymin = 33, xmax = 28, ymax = 34), fill = "red")
p <- p + geom_rect(aes(xmin = 31, ymin = 32, xmax = 32, ymax = 33), fill = "red")
p <- p + geom_rect(aes(xmin = 35, ymin = 31, xmax = 36, ymax = 32), fill = "red")
p <- p + geom_rect(fill = "#006600", aes(xmin = 22, ymin = 34, xmax = 23, ymax = 35), fill = "red")
p <- p + geom_rect(fill = "#006600", aes(xmin = 27, ymin = 33, xmax = 28, ymax = 34), fill = "red")
p <- p + geom_rect(fill = "#006600", aes(xmin = 31, ymin = 32, xmax = 32, ymax = 33), fill = "red")
p <- p + geom_rect(fill = "#006600", aes(xmin = 35, ymin = 31, xmax = 36, ymax = 32), fill = "red")
#Add labels
p <- p + annotate("text", label = "Transcript", x = 20, xmin = 10, y = 51.5, size = 5)
p <- p + annotate("text", label = "Transcript annotation", x = 20, xmin = 10, y = 46.5, size = 5)
p <- p + annotate("text", label = "Variants", x = 20, xmin = 10, y = 36.5, size = 5)
p <- p + annotate("text", label = "Annotations", x = 45, xmin = 44, y = 36.5, size = 5)
p <- p + annotate("text", label = "Distance=6;", x = 44, xmin = 44, y = 34.6, size = 4)
p <- p + annotate("text", label = "Distance=2;splicing_exonic", x = 48.5, xmin = 40, y = 33.6, size = 4)
p <- p + annotate("text", label = "Distance=2;splicing_intronic", x = 48.8, xmin = 40, y = 32.6, size = 4)
p <- p + annotate("text", label = "Distance=5;", x = 44, xmin = 44, y = 31.6, size = 4)
p <- p + annotate("text", label = "Distance=1;splicing_intronic", x = 48.8, xmin = 40, y = 32.6, size = 4)
p <- p + annotate("text", label = "Distance=4;", x = 44, xmin = 44, y = 31.6, size = 4)
#Add lines to make it clear
p <- p + geom_vline(xintercept = 30, linetype = "longdash") + geom_vline(xintercept = 40, linetype = "longdash")
print(p)
ggsave("variant_annotation_examples.png")
ggsave("variant_annotation_examples.pdf")
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