Final formatting

icbi-lab · Oct 7, 2023 · 858243d · 858243d
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diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 ## Kirchmair et al., Frontiers in Immunology 2023
 
-Data analyses for _<sup>13</sup>C tracer analysis reveals the landscape of metabolic checkpoints in human CD8<sup>+</sup> T cell differentiation and exhaustion (Kirchmair et al., Frontiers in Immunology 2023)_
+Data analyses for _<sup>13</sup>C tracer analysis reveals the landscape of metabolic checkpoints in human CD8<sup>+</sup> T cell differentiation and exhaustion_ (Kirchmair et al., Frontiers in Immunology 2023)
 
 
 

diff --git a/analyses/01-RNA-Differentiation.Rmd b/analyses/01-RNA-Differentiation.Rmd
@@ -6,7 +6,6 @@ params:
 ---
 
 ```{r setup, include=FALSE}
-
 library(datamisc)
 library(DESeq2)
 library(ggplot2)
@@ -16,7 +15,6 @@ library(GEOquery)
 library(clusterProfiler)
 
 dir.create("../data/rnaseq", showWarnings = FALSE)
-
 ```
 
 

diff --git a/analyses/02-13C-Differentiation.Rmd b/analyses/02-13C-Differentiation.Rmd
@@ -6,7 +6,6 @@ params:
 ---
 
 ```{r setup, include=FALSE}
-
 library(c13ms)
 library(datamisc)
 library(dplyr)
@@ -15,7 +14,6 @@ library(ggplot2)
 
 dir.create("../data/metabolomics", showWarnings = FALSE)
 dir.create(params$results, showWarnings = FALSE)
-
 ```
 
 

diff --git a/analyses/03-RNA-Exhaustion.Rmd b/analyses/03-RNA-Exhaustion.Rmd
@@ -6,7 +6,6 @@ params:
 ---
 
 ```{r setup, include=FALSE}
-
 library(datamisc)
 library(DESeq2)
 library(ggplot2)
@@ -16,7 +15,6 @@ library(GEOquery)
 library(clusterProfiler)
 
 dir.create("../data/rnaseq", showWarnings = FALSE)
-
 ```
 
 

diff --git a/analyses/04-13C-Exhaustion.Rmd b/analyses/04-13C-Exhaustion.Rmd
@@ -7,15 +7,13 @@ params:
 
 
 ```{r setup, include=FALSE}
-
 library(c13ms)
 library(datamisc)
 library(dplyr)
 library(openxlsx)
 
 dir.create("../data/metabolomics", showWarnings = FALSE)
 dir.create(params$results, showWarnings = FALSE)
-
 ```
 
 

diff --git a/analyses/05-RNA-Exhaustion-Public.Rmd b/analyses/05-RNA-Exhaustion-Public.Rmd
@@ -11,7 +11,6 @@ library(DESeq2)
 library(datamisc)
 
 dir.create(params$data, showWarnings = FALSE)
-
 ```
 
 

diff --git a/analyses/06-RNA-Mitochondria.Rmd b/analyses/06-RNA-Mitochondria.Rmd
@@ -18,7 +18,6 @@ library(TCGAbiolinks)
 dir.create(params$data, showWarnings = FALSE)
 if (!exists("mitodata"))  mitodata <- list()
 if (!exists("mitogenes"))  mitogenes <- list()
-
 ```
 
 
@@ -234,7 +233,8 @@ linmod <- lm(tumor_copy_number ~ ., data = ndata[,sel])
 selmod <- step(linmod, trace = FALSE, steps = 10000)
 summary(selmod)
 
-mitomodel$fit <- selmod
+mitomodel$linmod <- linmod
+mitomodel$selmod <- selmod
 ```
 
 

diff --git a/analyses/08-Results.Rmd b/analyses/08-Results.Rmd
@@ -10,7 +10,6 @@ params:
 ---
 
 ```{r setup, include=FALSE}
-
 library(ggplot2)
 library(c13ms)
 library(patchwork)
@@ -25,7 +24,6 @@ dir.create(params$figures, showWarnings = FALSE)
 dir.create(params$tables, showWarnings = FALSE)
 
 source("../lib/R-functions.R")
-
 ```
 
 
@@ -228,22 +226,22 @@ C13cells <- subset(C13mem, Sampletype == "cells")
 Plots
 ```{r}
 
-# dir.create(fp(params$figures, "isoplots"), showWarnings = FALSE)
-# 
-# C13cells |>
-#   isoplot(summarise_by = Celltype, assay = "mid_clean",
-#           col_cex = 0.5, linewidth = 2, nacolor = "white", colorscale = c("white", "#1702a1"),
-#           dir = fp(params$figures, "isoplots"), title = "ID", height = 10, title_size = 120, fontsize = 100,
-#           dev = "pdf", label = FALSE, cumulative = TRUE, legend = FALSE)
-# 
-# # plot legend
-# leg_plot <- C13cells |>
-#   isoplot(summarise_by = Celltype, assay = "mid_clean", mets = "lac", fontsize = 120, colorscale = c("white", "#1702a1"))
-# leg_plot <- leg_plot + theme_basic() + theme(plot.background = element_blank(), panel.background = element_blank(), legend.background = element_blank()) +
-#   guides(fill = guide_colourbar(barheight = grid::unit(200, "mm"), barwidth = grid::unit(20, "mm"), raster = FALSE, nbin = 20,
-#                                 ticks.colour = "black", frame.colour = "black", ticks.linewidth = 0.5, frame.linewidth = 0.5))
-# cowplot::get_legend(leg_plot) |>
-#   cowplot::ggsave2(filename = fp(params$figures, "isoplots", "legend.pdf"), dev = "pdf", width = 10, height = 20)
+dir.create(fp(params$figures, "isoplots"), showWarnings = FALSE)
+
+C13cells |>
+  isoplot(summarise_by = Celltype, assay = "mid_clean",
+          col_cex = 0.5, linewidth = 2, nacolor = "white", colorscale = c("white", "#1702a1"),
+          dir = fp(params$figures, "isoplots"), title = "ID", height = 10, title_size = 120, fontsize = 100,
+          dev = "pdf", label = FALSE, cumulative = TRUE, legend = FALSE)
+
+# plot legend
+leg_plot <- C13cells |>
+  isoplot(summarise_by = Celltype, assay = "mid_clean", mets = "lac", fontsize = 120, colorscale = c("white", "#1702a1"))
+leg_plot <- leg_plot + theme_basic() + theme(plot.background = element_blank(), panel.background = element_blank(), legend.background = element_blank()) +
+  guides(fill = guide_colourbar(barheight = grid::unit(200, "mm"), barwidth = grid::unit(20, "mm"), raster = FALSE, nbin = 20,
+                                ticks.colour = "black", frame.colour = "black", ticks.linewidth = 0.5, frame.linewidth = 0.5))
+cowplot::get_legend(leg_plot) |>
+  cowplot::ggsave2(filename = fp(params$figures, "isoplots", "legend.pdf"), dev = "pdf", width = 10, height = 20)
 
 ```
Original file line number	Diff line number	Diff line change
Expand Up		@@ -11,7 +11,6 @@ library(DESeq2)
		library(datamisc)

		dir.create(params$data, showWarnings = FALSE)

		```


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