Figure S3
Paul Hook
Last update: 2018-01-18
Code version: 5996c19850dc5fc65723f30bc33ab1c8d083a7e6
Setting important directories.
Also loading important libraries and custom functions for analysis.
seq_dir <- "/Volumes/PAULHOOK/sc-da-parkinsons/data"
file_dir <- "/Volumes/PAULHOOK/sc-da-parkinsons/output"
Rdata_dir <- "/Volumes/PAULHOOK/sc-da-parkinsons/data"
Script_dir <- "/Volumes/PAULHOOK/sc-da-parkinsons/code"
source(file.path(Script_dir,'init.R'))
source(file.path(Script_dir,"tools_R.r"))
#loading any special libraries
library(readr)
library(cowplot)theme <- theme(axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.y = element_text(family="Helvetica",size=8),
axis.text.y = element_text(size=6),
strip.text = element_text(family="Helvetica",face="bold.italic",size=10))P7.Fb.dat.filter <- readRDS(file.path(Rdata_dir,"P7.Fb.dat.filter.final.Rds"))
P7.Ob.dat.filter <- readRDS(file.path(Rdata_dir,"P7.Ob.dat.filter.final.Rds"))
e15.dat.filter <- readRDS(file.path(Rdata_dir,"e15.dat.filter.final.rds"))
e15.Fb.dat.filter <- readRDS(file.path(Rdata_dir,"e15.Fb.dat.filter.final.rds"))
e15.Mb.dat.filter <- readRDS(file.path(Rdata_dir,"e15.Mb.dat.filter.final.rds"))
color.all <- c("#F6937A","#882F1C","#BF1F36","#C2B280","#F2C318","#E790AC","#F18421","#0168A5","#848483","#A4CAEB","#885793","#008957","#222222")
color.P7 <- c("#F2C318","#E790AC","#F18421","#0168A5","#848483","#A4CAEB","#885793","#008957","#222222")Figure S3A
Plotting E15.5 t-SNE results colored by regional identity as well as subset cluster identity
#t-SNE plot colored by region
r <- myTSNEPlotAlpha(e15.dat.filter,color="region", shape="age") +
scale_color_brewer(palette="Set1", name = "Region") +
xlab("t-SNE 1") + ylab("t-SNE 2") +
theme(legend.position = "bottom",
axis.line = element_line(colour = "black"),
plot.title = element_text(hjust = 0.5),
axis.title = element_text(family='Helvetica',size=12)) +
coord_fixed(ratio = 1) + guides(shape=FALSE)
#t-SNE plot colored by subset cluster
c <- myTSNEPlotAlpha(e15.dat.filter,color="subset.cluster", shape="age") + scale_color_manual(values=color.all[1:4], name = "Subset Cluster") +
xlab("t-SNE 1") +
theme(legend.position = "bottom",
axis.line = element_line(colour = "black"),
plot.title = element_text(hjust = 0.5),
axis.title.y=element_blank(),
axis.title = element_text(family='Helvetica',size=12)) +
coord_fixed(ratio = 1) + guides(shape=FALSE)
# Plotting these in a grid
plot_grid(r,c,nrow = 1,ncol = 2)
# Writing out to PDF
pdf(file = file.path(file_dir, "Figure.S3A.pdf"), width = 7, height = 6)
r
c
dev.off()## quartz_off_screen
## 2Figure S3B
#t-SNE plot colored by region
s3b <- myTSNEPlotAlpha(e15.Fb.dat.filter,color="kmeans_tSNE_cluster", shape="age") + scale_color_manual(values=color.all[1:2], name = "Subset Cluster") +
xlab("t-SNE 1") + ylab("t-SNE 2") +
theme(legend.position = "bottom",
axis.line = element_line(colour = "black"),
plot.title = element_text(hjust = 0.5),
axis.title = element_text(family='Helvetica',size=10)) +
coord_fixed(ratio = 1) + guides(shape=FALSE) +
annotate('text',x=-180,y=325,label="Post-mitotic FB\nTh+ neurons",fontface=2,size=3) +
annotate('text',x=-250,y=-275,label="FB neuroblast",fontface=2,size=3)
pdf(file = file.path(file_dir, "Figure.S3B.pdf"), height = 5, width = 5)
s3b
dev.off()## quartz_off_screen
## 2s3b
Figure S3C
#t-SNE plot colored by region
s3c <- myTSNEPlotAlpha(e15.Mb.dat.filter,color="kmeans_tSNE_cluster", shape="age") + scale_color_manual(values=color.all[3:4], name = "Subset Cluster") +
xlab("t-SNE 1") + ylab("t-SNE 2") +
theme(legend.position = "bottom",
axis.line = element_line(colour = "black"),
plot.title = element_text(hjust = 0.5),
axis.title = element_text(family='Helvetica',size=10)) +
coord_fixed(ratio = 1) + guides(shape=FALSE) +
annotate('text',x=150,y=225,label="MB neuroblast",fontface=2,size=3) +
annotate('text',x=100,y=-250,label="Post-mitotic MB\nDA neurons",fontface=2,size=3)
pdf(file = file.path(file_dir, "Figure.S3C.pdf"), height = 5, width = 5)
s3c
dev.off()## quartz_off_screen
## 2s3c
Figure S3D
one <- myBoxplot.cluster(P7.Fb.dat.filter, "Onecut2", logMode = T) + scale_fill_manual(values = color.P7[1:2], name = "P7 FB Cluster") + theme
arx <- myBoxplot.cluster(P7.Fb.dat.filter, "Arx", logMode = T) + scale_fill_manual(values = color.P7[1:2], name = "P7 FB Cluster") + scale_y_continuous(breaks = c(0,1,2,3)) + theme
prlr <- myBoxplot.cluster(P7.Fb.dat.filter, "Prlr", logMode = T) + scale_fill_manual(values = color.P7[1:2], name = "P7 FB Cluster") + scale_y_continuous(breaks = c(0,1,2,3)) + theme
slc <- myBoxplot.cluster(P7.Fb.dat.filter, "Slc6a3", logMode = T) + scale_fill_manual(values = color.P7[1:2], name = "P7 FB Cluster") + theme
sst <- myBoxplot.cluster(P7.Fb.dat.filter, "Sst", logMode = T) + scale_fill_manual(values = color.P7[1:2], name = "P7 FB Cluster") + scale_y_continuous(breaks = c(0,2,4,6,8)) + theme
grid_arrange_shared_legend(one,arx,prlr,slc,sst,ncol=1,nrow=5, position = "bottom")
pdf(file = file.path(file_dir, "Figure.S3D.pdf"), height = 2, width = 4)
one
arx
prlr
slc
sst
dev.off()## quartz_off_screen
## 2Figure S3E
pax <- myBoxplot.cluster(P7.Ob.dat.filter, "Pax6", logMode = T) + scale_fill_manual(values = color.P7[7:9], name = "P7 OB Cluster") + theme
meis <- myBoxplot.cluster(P7.Ob.dat.filter, "Meis2", logMode = T) + scale_fill_manual(values = color.P7[7:9], name = "P7 OB Cluster") + theme
nr <- myBoxplot.cluster(P7.Ob.dat.filter, "Nr4a2", logMode = T) + scale_fill_manual(values = color.P7[7:9], name = "P7 OB Cluster") + theme
slc6 <- myBoxplot.cluster(P7.Ob.dat.filter, "Slc6a3", logMode = T) + scale_fill_manual(values = color.P7[7:9], name = "P7 OB Cluster") + theme
slc18 <- myBoxplot.cluster(P7.Ob.dat.filter, "Slc18a2", logMode = T) + scale_fill_manual(values = color.P7[7:9], name = "P7 OB Cluster") + theme
th <- myBoxplot.cluster(P7.Ob.dat.filter, "Th", logMode = T) + scale_fill_manual(values = color.P7[7:9], name = "P7 OB Cluster") + theme
ddc <- myBoxplot.cluster(P7.Ob.dat.filter, "Ddc", logMode = T) + scale_fill_manual(values = color.P7[7:9], name = "P7 OB Cluster") + theme
snap <- myBoxplot.cluster(P7.Ob.dat.filter, "Snap25", logMode = T) + scale_fill_manual(values = color.P7[7:9], name = "P7 OB Cluster") + theme
dcx <- myBoxplot.cluster(P7.Ob.dat.filter, "Dcx", logMode = T) + scale_fill_manual(values = color.P7[7:9], name = "P7 OB Cluster") + theme
grid_arrange_shared_legend(dcx,th,snap,ddc,pax,slc18,meis,slc6,nr,ncol=2,nrow=5, position = "bottom")
pdf(file = file.path(file_dir, "Figure.S3E.pdf"), height = 2, width = 4)
dcx
snap
pax
meis
nr
th
ddc
slc18
slc6
dev.off()## quartz_off_screen
## 2Session Info
sessionInfo()## R version 3.3.0 (2016-05-03)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: OS X 10.11.6 (El Capitan)
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] grid splines stats4 parallel stats graphics grDevices
## [8] utils datasets methods base
##
## other attached packages:
## [1] cowplot_0.9.2 readr_1.1.1 ggbiplot_0.55
## [4] scales_0.5.0 SC3_1.1.4 ROCR_1.0-7
## [7] jackstraw_1.1.1 lfa_1.2.2 tsne_0.1-3
## [10] gridExtra_2.3 slackr_1.4.2 vegan_2.4-4
## [13] permute_0.9-4 MASS_7.3-47 gplots_3.0.1
## [16] RColorBrewer_1.1-2 Hmisc_4.0-3 Formula_1.2-2
## [19] survival_2.41-3 lattice_0.20-35 Heatplus_2.18.0
## [22] Rtsne_0.13 pheatmap_1.0.8 tidyr_0.7.1
## [25] dplyr_0.7.4 plyr_1.8.4 heatmap.plus_1.3
## [28] stringr_1.2.0 marray_1.50.0 limma_3.28.21
## [31] reshape2_1.4.3 monocle_2.2.0 DDRTree_0.1.5
## [34] irlba_2.2.1 VGAM_1.0-2 ggplot2_2.2.1
## [37] Biobase_2.32.0 BiocGenerics_0.18.0 Matrix_1.2-11
##
## loaded via a namespace (and not attached):
## [1] RSelenium_1.7.1 colorspace_1.3-2 class_7.3-14
## [4] rprojroot_1.2 htmlTable_1.9 corpcor_1.6.9
## [7] base64enc_0.1-3 mvtnorm_1.0-6 codetools_0.2-15
## [10] doParallel_1.0.11 robustbase_0.92-7 knitr_1.17
## [13] jsonlite_1.5 cluster_2.0.6 semver_0.2.0
## [16] shiny_1.0.5 rrcov_1.4-3 httr_1.3.1
## [19] backports_1.1.1 assertthat_0.2.0 lazyeval_0.2.1
## [22] acepack_1.4.1 htmltools_0.3.6 tools_3.3.0
## [25] bindrcpp_0.2 igraph_1.1.2 gtable_0.2.0
## [28] glue_1.1.1 binman_0.1.0 doRNG_1.6.6
## [31] Rcpp_0.12.14 slam_0.1-37 gdata_2.18.0
## [34] nlme_3.1-131 iterators_1.0.8 mime_0.5
## [37] rngtools_1.2.4 gtools_3.5.0 WriteXLS_4.0.0
## [40] XML_3.98-1.9 DEoptimR_1.0-8 hms_0.3
## [43] yaml_2.1.15 pkgmaker_0.22 rpart_4.1-11
## [46] fastICA_1.2-1 latticeExtra_0.6-28 stringi_1.1.5
## [49] pcaPP_1.9-72 foreach_1.4.3 e1071_1.6-8
## [52] checkmate_1.8.4 caTools_1.17.1 rlang_0.1.6
## [55] pkgconfig_2.0.1 matrixStats_0.52.2 bitops_1.0-6
## [58] qlcMatrix_0.9.5 evaluate_0.10.1 purrr_0.2.4
## [61] bindr_0.1 labeling_0.3 htmlwidgets_0.9
## [64] magrittr_1.5 R6_2.2.2 combinat_0.0-8
## [67] wdman_0.2.2 foreign_0.8-69 mgcv_1.8-22
## [70] nnet_7.3-12 tibble_1.3.4 KernSmooth_2.23-15
## [73] rmarkdown_1.8 data.table_1.10.4 HSMMSingleCell_0.106.2
## [76] digest_0.6.12 xtable_1.8-2 httpuv_1.3.5
## [79] openssl_0.9.7 munsell_0.4.3 registry_0.3This R Markdown site was created with workflowr