rearrange files

hemberg-lab · Feb 27, 2017 · 1840aa6 · 1840aa6
1 parent a305ea4
commit 1840aa6
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Showing 31 changed files with 43 additions and 42 deletions.
diff --git a/.gitignore b/.gitignore
@@ -3,3 +3,4 @@
 .RData
 .Ruserdata
 *.Rproj
+Rplots.pdf
diff --git a/1c.R b/1c.R
@@ -3,7 +3,7 @@ library(dplyr)
 
 options(stringsAsFactors = FALSE)
 
-d <- read.csv("1c.csv")
+d <- read.csv("data/1c.csv")
 
 d$Dataset <- factor(
     d$Dataset, 
@@ -24,5 +24,5 @@ p <- ggplot(d, aes(d, fill = Dataset)) +
     labs(x = "d as % of N", y = "# of solutions with ARI > 95% of max.") +
     theme_classic(base_size = 14)
 
-ggsave("1c.pdf", w = 6, h = 4.5)
-ggsave("1c.jpeg", w = 6, h = 4.5)
+ggsave("pdf/1c.pdf", w = 6, h = 4.5)
+ggsave("jpeg/1c.jpeg", w = 6, h = 4.5)
diff --git a/1d.R b/1d.R
@@ -18,7 +18,7 @@ gtable_stack <- function(g1, g2){
     g1
 }
 
-d <- read.csv("1d.csv")
+d <- read.csv("data/1d.csv")
 
 d[d$Dataset == "Kolodziejczyk", ]$Dataset <- "Kolodz."
 
@@ -81,5 +81,5 @@ new_plot <- gtable_stack(g1, new_strips)
 
 plot_grid(new_plot)
 
-ggsave("1d.pdf", w = 6.3, h = 4.5)
-ggsave("1d.jpeg", w = 6.3, h = 4.5)
+ggsave("pdf/1d.pdf", w = 6.3, h = 4.5)
+ggsave("jpeg/1d.jpeg", w = 6.3, h = 4.5)
diff --git a/1d.pdf b/1d.pdf
diff --git a/README.md b/README.md
@@ -7,44 +7,44 @@ This repository contains scripts for recreation of the figures from the SC3 pape
 [dplyr](https://cran.r-project.org/web/packages/dplyr/index.html)
 
 ### Fig. 1
-[data_c](1c.csv)  
+[data_c](data/1c.csv)  
 [script](1c.R)  
-[pdf](1c.pdf)  
-![](1c.jpeg)
+[pdf](pdf/1c.pdf)  
+![](jpeg/1c.jpeg)
 
-[data_d](1d.csv)  
+[data_d](data/1d.csv)  
 [script](1d.R)  
-[pdf](1d.pdf)  
-![](1d.jpeg)
+[pdf](pdf/1d.pdf)  
+![](jpeg/1d.jpeg)
 
 ### Fig. S1
 
-[data](S1.csv)  
+[data](data/S1.csv)  
 [script](S1.R)  
-![](S1.jpeg)
+![](jpeg/S1.jpeg)
 
 ### Fig. S2
 
-[data](S2.csv)  
+[data](data/S2.csv)  
 [script](S2.R)  
-![](S2.jpeg)
+![](jpeg/S2.jpeg)
 
 ### Fig. S3
-[data_a](S3a.csv)  
-[data_b](S3b.csv)  
-[data_c](S3c.csv)  
-[data_d](S3d.csv)  
+[data_a](data/S3a.csv)  
+[data_b](data/S3b.csv)  
+[data_c](data/S3c.csv)  
+[data_d](data/S3d.csv)  
 [script](S3.R)  
-![](S3.jpeg)
+![](jpeg/S3.jpeg)
 
 ### Fig. S4
-[data_a](S4a.csv)  
-[data_b](S4b.csv)  
-[data_c](S4c.csv)  
-[data_d](S4d.csv)  
-[data_e](S4e.csv)  
+[data_a](data/S4a.csv)  
+[data_b](data/S4b.csv)  
+[data_c](data/S4c.csv)  
+[data_d](data/S4d.csv)  
+[data_e](data/S4e.csv)  
 [script](S4.R)  
-![](S4.jpeg)
+![](jpeg/S4.jpeg)
 
 ## Session Info
 

diff --git a/S1.R b/S1.R
@@ -3,7 +3,7 @@ library(dplyr)
 
 options(stringsAsFactors = FALSE)
 
-d <- read.csv("S1.csv")
+d <- read.csv("data/S1.csv")
 
 d_med <- d %>%
     group_by(Dataset, gene_filter, Distance, Transformation, d) %>%
@@ -25,4 +25,4 @@ p <- ggplot(d, aes(d, ARI, group = Group, color = Transformation)) +
     annotate("segment", x=-Inf, xend=Inf, y=-Inf, yend=-Inf, color = "black")+
     annotate("segment", x=-Inf, xend=-Inf, y=-Inf, yend=Inf, color = "black")
 
-ggsave("S1.jpeg", w = 9, h = 6)
+ggsave("jpeg/S1.jpeg", w = 9, h = 6)
diff --git a/S2.R b/S2.R
@@ -3,7 +3,7 @@ library(dplyr)
 
 options(stringsAsFactors = FALSE)
 
-d <- read.csv("S2.csv")
+d <- read.csv("data/S2.csv")
 
 d_med <- d %>%
     group_by(Dataset, gene_filter, Distance, Transformation, d) %>%
@@ -25,4 +25,4 @@ p <- ggplot(d, aes(d, ARI, group = Group, color = Transformation)) +
     annotate("segment", x=-Inf, xend=Inf, y=-Inf, yend=-Inf, color = "black")+
     annotate("segment", x=-Inf, xend=-Inf, y=-Inf, yend=Inf, color = "black")
 
-ggsave("S2.jpeg", w = 9, h = 6)
+ggsave("jpeg/S2.jpeg", w = 9, h = 6)
diff --git a/S3.R b/S3.R
@@ -5,7 +5,7 @@ options(stringsAsFactors = FALSE)
 font_size <- 6
 
 get_a <- function() {
-    d <- read.csv("S3a.csv")
+    d <- read.csv("data/S3a.csv")
 
     d$Dataset <- factor(
         d$Dataset, 
@@ -29,7 +29,7 @@ get_a <- function() {
 }
 
 get_b <- function() {
-    d <- read.csv("S3b.csv")
+    d <- read.csv("data/S3b.csv")
 
     d$Dataset <- factor(
         d$Dataset, 
@@ -53,7 +53,7 @@ get_b <- function() {
 }
 
 get_c <- function() {
-    d <- read.csv("S3c.csv")
+    d <- read.csv("data/S3c.csv")
 
     d$Dataset <- factor(
         d$Dataset, 
@@ -125,7 +125,7 @@ get_d <- function() {
               "Usoskin3" = "#fdb462", "Kolodziejczyk" = "#bf812d",
               "Klein" = "#b3de69", "Zeisel" = "#fccde5")
 
-    d <- read.csv("S3d.csv")
+    d <- read.csv("data/S3d.csv")
 
     d$Hierarchy <- factor(
         d$Hierarchy, 
@@ -178,4 +178,4 @@ get_d <- function() {
 
 plot_grid(get_a(), get_b(), get_c(), get_d(), ncol = 2, labels = c("a", "b", "c", "d"), rel_heights = c(1, 1.8))
 
-ggsave("S3.jpeg", w = 9, h = 6)
+ggsave("jpeg/S3.jpeg", w = 9, h = 6)
diff --git a/S3.jpeg b/S3.jpeg
diff --git a/S4.R b/S4.R
@@ -5,7 +5,7 @@ options(stringsAsFactors = FALSE)
 font_size <- 7
 
 get_a <- function() {
-    d <- read.csv("S4a.csv")
+    d <- read.csv("data/S4a.csv")
     d$group <- paste(d$nstart, d$Method)
     d$Method <- factor(
         d$Method, 
@@ -45,7 +45,7 @@ get_b <- function() {
               "Usoskin3" = "#fdb462", "Kolodziejczyk" = "#bf812d",
               "Klein" = "#b3de69", "Zeisel" = "#fccde5")
 
-    d <- read.csv("S4b.csv")
+    d <- read.csv("data/S4b.csv")
 
     d$Dataset <- factor(
         d$Dataset, 
@@ -101,7 +101,7 @@ get_c <- function() {
               "Kolodziejczyk" = "#bf812d", "Usoskin3" = "#fdb462",
               "Klein" = "#40E0D0", "Zeisel" = "#fccde5", "Macosko" = "#d9d9d9")
 
-    d <- read.csv("S4c.csv")
+    d <- read.csv("data/S4c.csv")
 
     d$Dataset <- factor(
         d$Dataset,
@@ -149,7 +149,7 @@ get_d <- function() {
     cols <- c("Pollen2" = "#fb8072",
               "Kolodziejczyk" = "#bf812d")
 
-    d <- read.csv("S4d.csv")
+    d <- read.csv("data/S4d.csv")
     d$Dataset <- factor(d$Dataset, levels <- c("Pollen2", "Kolodziejczyk"))
 
     limits <- aes(ymax = mean + se, ymin = mean - se)
@@ -168,7 +168,7 @@ get_e <- function() {
     cols <- c("Pollen2" = "#fb8072",
               "Kolodziejczyk" = "#bf812d")
 
-    d <- read.csv("S4e.csv")
+    d <- read.csv("data/S4e.csv")
     d$Dataset <- factor(d$Dataset, levels <- c("Pollen2", "Kolodziejczyk"))
 
     limits <- aes(ymax = mean + se, ymin = mean - se)
@@ -190,4 +190,4 @@ third_row <- plot_grid(get_d(), get_e(), ncol = 2, labels = c("d", "e"))
 
 plot_grid(first_row, second_row, third_row, nrow = 3)
 
-ggsave("S4.jpeg", w = 9, h = 6)
+ggsave("jpeg/S4.jpeg", w = 9, h = 6)
diff --git a/1c.csv → data/1c.csv b/1c.csv → data/1c.csv
diff --git a/1d.csv → data/1d.csv b/1d.csv → data/1d.csv
diff --git a/S1.csv → data/S1.csv b/S1.csv → data/S1.csv
diff --git a/S2.csv → data/S2.csv b/S2.csv → data/S2.csv
diff --git a/S3a.csv → data/S3a.csv b/S3a.csv → data/S3a.csv
diff --git a/S3b.csv → data/S3b.csv b/S3b.csv → data/S3b.csv
diff --git a/S3c.csv → data/S3c.csv b/S3c.csv → data/S3c.csv
diff --git a/S3d.csv → data/S3d.csv b/S3d.csv → data/S3d.csv
diff --git a/S4a.csv → data/S4a.csv b/S4a.csv → data/S4a.csv
diff --git a/S4b.csv → data/S4b.csv b/S4b.csv → data/S4b.csv
diff --git a/S4c.csv → data/S4c.csv b/S4c.csv → data/S4c.csv
diff --git a/S4d.csv → data/S4d.csv b/S4d.csv → data/S4d.csv
diff --git a/S4e.csv → data/S4e.csv b/S4e.csv → data/S4e.csv
diff --git a/1c.jpeg → jpeg/1c.jpeg b/1c.jpeg → jpeg/1c.jpeg
diff --git a/1d.jpeg → jpeg/1d.jpeg b/1d.jpeg → jpeg/1d.jpeg
diff --git a/S1.jpeg → jpeg/S1.jpeg b/S1.jpeg → jpeg/S1.jpeg
diff --git a/S2.jpeg → jpeg/S2.jpeg b/S2.jpeg → jpeg/S2.jpeg
diff --git a/jpeg/S3.jpeg b/jpeg/S3.jpeg
diff --git a/S4.jpeg → jpeg/S4.jpeg b/S4.jpeg → jpeg/S4.jpeg
diff --git a/1c.pdf → pdf/1c.pdf b/1c.pdf → pdf/1c.pdf
diff --git a/pdf/1d.pdf b/pdf/1d.pdf
-Original file line number
+Diff line change
@@ Expand Up / @@ -3,3 +3,4 @@ @@
     .RData
     .Ruserdata
     *.Rproj
+    Rplots.pdf