diff --git a/230313_cmQTL_val1_2_GC_met_rla_plot.jpg b/230313_cmQTL_val1_2_GC_met_rla_plot.jpg
deleted file mode 100644
index f6d7b3c8d8d864133870411edb3675a347aaf680..0000000000000000000000000000000000000000
Binary files a/230313_cmQTL_val1_2_GC_met_rla_plot.jpg and /dev/null differ
diff --git a/230313_cmQTL_val1_2_samples_rla_plot.jpg b/230313_cmQTL_val1_2_samples_rla_plot.jpg
deleted file mode 100644
index 143a587770b11547e8809b00084345093ae4dbb5..0000000000000000000000000000000000000000
Binary files a/230313_cmQTL_val1_2_samples_rla_plot.jpg and /dev/null differ
diff --git a/230313_cmQTL_val1_batch_imp_PCA.jpg b/230313_cmQTL_val1_batch_imp_PCA.jpg
deleted file mode 100644
index 35477ad863ad9ddc53de4df7f3c721f174e06f6a..0000000000000000000000000000000000000000
Binary files a/230313_cmQTL_val1_batch_imp_PCA.jpg and /dev/null differ
diff --git a/230313_cmQTL_val1_class_imp_PCA.jpg b/230313_cmQTL_val1_class_imp_PCA.jpg
deleted file mode 100644
index b72fd0531a873787004673c8a1978ce9b1f57a45..0000000000000000000000000000000000000000
Binary files a/230313_cmQTL_val1_class_imp_PCA.jpg and /dev/null differ
diff --git a/230313_cmQTL_val1_fruit_treatment_loess_PCA.jpg b/230313_cmQTL_val1_fruit_treatment_loess_PCA.jpg
deleted file mode 100644
index 90c2504331e3e4eb6696e15e00bd13f8ccf8f6da..0000000000000000000000000000000000000000
Binary files a/230313_cmQTL_val1_fruit_treatment_loess_PCA.jpg and /dev/null differ
diff --git a/230313_cmQTL_val1_leaf_treatment_loess_PCA.jpg b/230313_cmQTL_val1_leaf_treatment_loess_PCA.jpg
deleted file mode 100644
index 8927e2b3cf79b7bffb5a99d3b1d52fe6fa8907d0..0000000000000000000000000000000000000000
Binary files a/230313_cmQTL_val1_leaf_treatment_loess_PCA.jpg and /dev/null differ
diff --git a/230313_cmQTL_val1_tissue_imp_PCA.jpg b/230313_cmQTL_val1_tissue_imp_PCA.jpg
deleted file mode 100644
index 729c414ef28a035d73db4e8374c24094767bb049..0000000000000000000000000000000000000000
Binary files a/230313_cmQTL_val1_tissue_imp_PCA.jpg and /dev/null differ
diff --git a/230313_cmQTL_val1_tissue_lin_PCA.jpg b/230313_cmQTL_val1_tissue_lin_PCA.jpg
deleted file mode 100644
index ed060f270f74645ff152820ec4401f48a4121502..0000000000000000000000000000000000000000
Binary files a/230313_cmQTL_val1_tissue_lin_PCA.jpg and /dev/null differ
diff --git a/230313_cmQTL_val1_tissue_loess_PCA.jpg b/230313_cmQTL_val1_tissue_loess_PCA.jpg
deleted file mode 100644
index 10cfd249bc7c2551f7393dff512b14ea7c1e9ffa..0000000000000000000000000000000000000000
Binary files a/230313_cmQTL_val1_tissue_loess_PCA.jpg and /dev/null differ
diff --git a/230313_cmQTL_val1_treatment_PCA.jpg b/230313_cmQTL_val1_treatment_PCA.jpg
deleted file mode 100644
index 4a8313dd5dc1c092e094b686e0b50bba4d8a2c49..0000000000000000000000000000000000000000
Binary files a/230313_cmQTL_val1_treatment_PCA.jpg and /dev/null differ
diff --git a/230313_cmQTL_val1_treatment_loess_PCA.jpg b/230313_cmQTL_val1_treatment_loess_PCA.jpg
deleted file mode 100644
index cf488b11c19ebea36f3f4a6686cc56024bc72f4c..0000000000000000000000000000000000000000
Binary files a/230313_cmQTL_val1_treatment_loess_PCA.jpg and /dev/null differ
diff --git a/230313_cmQTL_val1_treatment_loess_outlier_exp1_PCA.jpg b/230313_cmQTL_val1_treatment_loess_outlier_exp1_PCA.jpg
deleted file mode 100644
index 8a0493bbcb5991cab0e77a86983d541aca4065d3..0000000000000000000000000000000000000000
Binary files a/230313_cmQTL_val1_treatment_loess_outlier_exp1_PCA.jpg and /dev/null differ
diff --git a/230313_cmQTL_val1_treatment_loess_outlier_exp2_imp_PCA.jpg b/230313_cmQTL_val1_treatment_loess_outlier_exp2_imp_PCA.jpg
deleted file mode 100644
index a0051be5d5cab588a0a458cb52cc9ba269d9d911..0000000000000000000000000000000000000000
Binary files a/230313_cmQTL_val1_treatment_loess_outlier_exp2_imp_PCA.jpg and /dev/null differ
diff --git a/230313_cmQTL_val1_treatment_loess_outlier_exp2_loess_norm_PCA.jpg b/230313_cmQTL_val1_treatment_loess_outlier_exp2_loess_norm_PCA.jpg
deleted file mode 100644
index d52d65d709decaea3151018059f94265cd9297eb..0000000000000000000000000000000000000000
Binary files a/230313_cmQTL_val1_treatment_loess_outlier_exp2_loess_norm_PCA.jpg and /dev/null differ
diff --git a/230313_cmQTL_val2_class_isnorm_PCA.jpg b/230313_cmQTL_val2_class_isnorm_PCA.jpg
deleted file mode 100644
index af3a3d094956052c7c7aeb56a9cbff736fa2f3b4..0000000000000000000000000000000000000000
Binary files a/230313_cmQTL_val2_class_isnorm_PCA.jpg and /dev/null differ
diff --git a/230313_linnorm.pdf b/230313_linnorm.pdf
deleted file mode 100644
index 7fb1c2d37b079e791a457827933a6bc2595c21a1..0000000000000000000000000000000000000000
Binary files a/230313_linnorm.pdf and /dev/null differ
diff --git a/230313_loess_fit.pdf b/230313_loess_fit.pdf
deleted file mode 100644
index acd410af368debcbd2e2ddad54fa4625d793becd..0000000000000000000000000000000000000000
Binary files a/230313_loess_fit.pdf and /dev/null differ
diff --git a/230313_loess_norm_fw_log.pdf b/230313_loess_norm_fw_log.pdf
deleted file mode 100644
index 76e9279965d6f7ed0e1d911828382161b28c5bea..0000000000000000000000000000000000000000
Binary files a/230313_loess_norm_fw_log.pdf and /dev/null differ
diff --git a/230313_loess_norm_no_scale.pdf b/230313_loess_norm_no_scale.pdf
deleted file mode 100644
index cf30680c79aaa3bc327f0d285a7f7fa76912b8f1..0000000000000000000000000000000000000000
Binary files a/230313_loess_norm_no_scale.pdf and /dev/null differ
diff --git a/runs/GC-MS normalization/_linnorm.pdf b/runs/GC-MS normalization/_linnorm.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..a1b56f697faca85f53cffe087e10188020b487eb
Binary files /dev/null and b/runs/GC-MS normalization/_linnorm.pdf differ
diff --git a/runs/GC-MS normalization/_loess_fit.pdf b/runs/GC-MS normalization/_loess_fit.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..bd907e7c808daf905f2eb0c1fefbf4b6dd67cec7
Binary files /dev/null and b/runs/GC-MS normalization/_loess_fit.pdf differ
diff --git a/runs/GC-MS normalization/_loess_norm_fw_log.pdf b/runs/GC-MS normalization/_loess_norm_fw_log.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..a492791f0567d2695de7bfc0aebffd11767487b9
Binary files /dev/null and b/runs/GC-MS normalization/_loess_norm_fw_log.pdf differ
diff --git a/runs/GC-MS normalization/_loess_norm_no_scale.pdf b/runs/GC-MS normalization/_loess_norm_no_scale.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..d0eab2cc0a08350ee287e82656d9992acc32f877
Binary files /dev/null and b/runs/GC-MS normalization/_loess_norm_no_scale.pdf differ
diff --git a/runs/GC-MS normalization/cmQTL_val1/fruit/treatment_loess_PCA.jpg b/runs/GC-MS normalization/cmQTL_val1/fruit/treatment_loess_PCA.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..789d9d8d26208396f7a2535f46c55dde33d6a2eb
Binary files /dev/null and b/runs/GC-MS normalization/cmQTL_val1/fruit/treatment_loess_PCA.jpg differ
diff --git a/runs/GC-MS normalization/cmQTL_val1/leaf/treatment_loess_PCA.jpg b/runs/GC-MS normalization/cmQTL_val1/leaf/treatment_loess_PCA.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..e659cf390d18d9ca65f85fe4bec0043faf6410ce
Binary files /dev/null and b/runs/GC-MS normalization/cmQTL_val1/leaf/treatment_loess_PCA.jpg differ
diff --git a/runs/GC-MS normalization/cmQTL_val1_2_GC_met_rla_plot.jpg b/runs/GC-MS normalization/cmQTL_val1_2_GC_met_rla_plot.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..06b3542a0890dcdddecd65920ad49fb776d37e6b
Binary files /dev/null and b/runs/GC-MS normalization/cmQTL_val1_2_GC_met_rla_plot.jpg differ
diff --git a/runs/GC-MS normalization/cmQTL_val1_2_samples_rla_plot.jpg b/runs/GC-MS normalization/cmQTL_val1_2_samples_rla_plot.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..3183af762fd7b550d01f976017f1e26b10c88778
Binary files /dev/null and b/runs/GC-MS normalization/cmQTL_val1_2_samples_rla_plot.jpg differ
diff --git a/runs/GC-MS normalization/cmQTL_val1_batch_imp_PCA.jpg b/runs/GC-MS normalization/cmQTL_val1_batch_imp_PCA.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..bfb90fe7db1ec011aff8c1c5fa846dd028ff8dde
Binary files /dev/null and b/runs/GC-MS normalization/cmQTL_val1_batch_imp_PCA.jpg differ
diff --git a/runs/GC-MS normalization/cmQTL_val1_class_imp_PCA.jpg b/runs/GC-MS normalization/cmQTL_val1_class_imp_PCA.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..8bf923236138f1abd6da0478170f2059501ace7e
Binary files /dev/null and b/runs/GC-MS normalization/cmQTL_val1_class_imp_PCA.jpg differ
diff --git a/runs/GC-MS normalization/cmQTL_val1_tissue_imp_PCA.jpg b/runs/GC-MS normalization/cmQTL_val1_tissue_imp_PCA.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..585c8bc5615e1edcf65763edcb06b9d84dad3bfd
Binary files /dev/null and b/runs/GC-MS normalization/cmQTL_val1_tissue_imp_PCA.jpg differ
diff --git a/runs/GC-MS normalization/cmQTL_val1_tissue_lin_PCA.jpg b/runs/GC-MS normalization/cmQTL_val1_tissue_lin_PCA.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..faf8d896aedd0bd6a754d65e01b0af3aa7ea8149
Binary files /dev/null and b/runs/GC-MS normalization/cmQTL_val1_tissue_lin_PCA.jpg differ
diff --git a/runs/GC-MS normalization/cmQTL_val1_tissue_loess_PCA.jpg b/runs/GC-MS normalization/cmQTL_val1_tissue_loess_PCA.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..2cbbe7ed76721a8296bd43591e3f75a9d15e2a44
Binary files /dev/null and b/runs/GC-MS normalization/cmQTL_val1_tissue_loess_PCA.jpg differ
diff --git a/runs/GC-MS normalization/cmQTL_val1_treatment_PCA.jpg b/runs/GC-MS normalization/cmQTL_val1_treatment_PCA.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..fc6cbc86aa15983c3f60d9e081fe9609d01219be
Binary files /dev/null and b/runs/GC-MS normalization/cmQTL_val1_treatment_PCA.jpg differ
diff --git a/runs/GC-MS normalization/cmQTL_val1_treatment_loess_PCA.jpg b/runs/GC-MS normalization/cmQTL_val1_treatment_loess_PCA.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..585c72dbe95ad7565935212cf792b17ea91b0903
Binary files /dev/null and b/runs/GC-MS normalization/cmQTL_val1_treatment_loess_PCA.jpg differ
diff --git a/runs/GC-MS normalization/cmQTL_val1_treatment_loess_outlier_exp1_PCA.jpg b/runs/GC-MS normalization/cmQTL_val1_treatment_loess_outlier_exp1_PCA.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..2009c9ad376ef6f66ef4cf225379862907daf3e7
Binary files /dev/null and b/runs/GC-MS normalization/cmQTL_val1_treatment_loess_outlier_exp1_PCA.jpg differ
diff --git a/runs/GC-MS normalization/cmQTL_val1_treatment_loess_outlier_exp2_imp_PCA.jpg b/runs/GC-MS normalization/cmQTL_val1_treatment_loess_outlier_exp2_imp_PCA.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..5114cb5449c9d180cd337340f4b4f7f3f28992b2
Binary files /dev/null and b/runs/GC-MS normalization/cmQTL_val1_treatment_loess_outlier_exp2_imp_PCA.jpg differ
diff --git a/runs/GC-MS normalization/cmQTL_val1_treatment_loess_outlier_exp2_loess_norm_PCA.jpg b/runs/GC-MS normalization/cmQTL_val1_treatment_loess_outlier_exp2_loess_norm_PCA.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..f34ef7a03390e9da1dad9f6864016268a9a5f259
Binary files /dev/null and b/runs/GC-MS normalization/cmQTL_val1_treatment_loess_outlier_exp2_loess_norm_PCA.jpg differ
diff --git a/runs/GC-MS normalization/cmQTL_val2_class_isnorm_PCA.jpg b/runs/GC-MS normalization/cmQTL_val2_class_isnorm_PCA.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..62fcac95ef7682be33061aecdd854a6f74be4459
Binary files /dev/null and b/runs/GC-MS normalization/cmQTL_val2_class_isnorm_PCA.jpg differ
diff --git a/230313_cmQTL_val_1_2_feat_dat_GC.csv b/runs/GC-MS normalization/cmQTL_val_1_2_feat_dat_GC.csv
similarity index 100%
rename from 230313_cmQTL_val_1_2_feat_dat_GC.csv
rename to runs/GC-MS normalization/cmQTL_val_1_2_feat_dat_GC.csv
diff --git a/230313_cmQTL_val_1_2_met_dat_GC.csv b/runs/GC-MS normalization/cmQTL_val_1_2_met_dat_GC.csv
similarity index 100%
rename from 230313_cmQTL_val_1_2_met_dat_GC.csv
rename to runs/GC-MS normalization/cmQTL_val_1_2_met_dat_GC.csv
diff --git a/230313_cmQTL_val_1_2_miss_GC.csv b/runs/GC-MS normalization/cmQTL_val_1_2_miss_GC.csv
similarity index 100%
rename from 230313_cmQTL_val_1_2_miss_GC.csv
rename to runs/GC-MS normalization/cmQTL_val_1_2_miss_GC.csv
diff --git a/230313_cmQTL_val_1_2_sam_dat_GC.csv b/runs/GC-MS normalization/cmQTL_val_1_2_sam_dat_GC.csv
similarity index 100%
rename from 230313_cmQTL_val_1_2_sam_dat_GC.csv
rename to runs/GC-MS normalization/cmQTL_val_1_2_sam_dat_GC.csv
diff --git a/workflows/GC_MS_normalization/210927_primary_normalization_with_split.R b/workflows/GC_MS_normalization/210927_primary_normalization_with_split.R
index af50f96e935f7ed89e1ae21d3b6ec4092f679923..fb2c78b6c017b8983876102ce48a6cb21cdeff94 100644
--- a/workflows/GC_MS_normalization/210927_primary_normalization_with_split.R
+++ b/workflows/GC_MS_normalization/210927_primary_normalization_with_split.R
@@ -157,14 +157,6 @@ area <- area %>%
left_join(met_dat) %>%
mutate(area = as.numeric(area))
-#unique qc names tidier
-#arrange run_num gc and create daily_num or supply daily_num
- stop()
-
-
-
-setwd(out_dir)
-
# PCA to justify filtering ------------------------------------------------
features_pca <- area %>%
@@ -211,9 +203,8 @@ pca_plot %>%
ylab(str_c("PC2 ", "(", exp_var$PC2[[2]]*100, "%)")) +
xlab(str_c("PC1 ", "(", exp_var$PC1[[2]]*100, "%)"))
-ggsave(str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),
- "cmQTL_val1_treatment_loess_outlier_exp1_PCA.jpg",
- sep = "_"),
+ggsave(here(out,
+ "cmQTL_val1_treatment_loess_outlier_exp1_PCA.jpg"),
width = 183,
height = 100,
units = "mm",
@@ -259,9 +250,9 @@ pca_plot %>%
ylab(str_c("PC2 ", "(", exp_var$PC2[[2]]*100, "%)")) +
xlab(str_c("PC1 ", "(", exp_var$PC1[[2]]*100, "%)"))
-ggsave(str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),
- "cmQTL_val1_treatment_loess_outlier_exp2_imp_PCA.jpg",
- sep = "_"),
+ggsave(here(out,
+ "cmQTL_val1_treatment_loess_outlier_exp2_imp_PCA.jpg"
+ ),
width = 183,
height = 100,
units = "mm",
@@ -319,14 +310,14 @@ features_filtered <- area_long %>%
# Internal standard check -------------------------------------------------
features_filtered %>%
- filter(str_detect(Compound_Name, "ribitol")) %>%
+ filter(str_detect(component, "ribitol")) %>%
mutate(xint = if_else(daily_num == 4, run_num_GC-3.5, max(run_num_GC)),
is_miss = as_factor(if_else(is.na(area), T, F))) %>%
- filter(class!="blank") %>%
+ filter(class!="blank sample") %>%
ggplot(aes(x=run_num_GC, y = log2(imp))) +
geom_point(aes(color = class, shape = is_miss)) +
geom_vline(aes(xintercept = xint)) +
- facet_grid(rows = vars(Compound_Name))
+ facet_grid(rows = vars(component))
# Internal Standard Normalization -----------------------------------------
@@ -494,9 +485,9 @@ features_all %>%
theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
ylim(c(-2,2))
-ggsave(str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),
- "cmQTL_val1_2_GC_met_rla_plot.jpg",
- sep = "_"))
+ggsave(here(out,
+ "cmQTL_val1_2_GC_met_rla_plot.jpg"
+ ))
features_all %>%
#filter(!is.na(taxa)) %>%
@@ -514,9 +505,9 @@ features_all %>%
theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
ylim(c(-1,1))
-ggsave(str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),
- "cmQTL_val1_2_samples_rla_plot.jpg",
- sep = "_"))
+ggsave(here(out,
+ "cmQTL_val1_2_samples_rla_plot.jpg"
+ ))
# RSD estimation ----------------------------------------------------------
@@ -603,9 +594,9 @@ pca_plot %>%
ylab(str_c("PC2 ", "(", exp_var$PC2[[2]]*100, "%)")) +
xlab(str_c("PC1 ", "(", exp_var$PC1[[2]]*100, "%)"))
-ggsave(str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),
- "cmQTL_val1_tissue_lin_PCA.jpg",
- sep = "_"),
+ggsave(here(out,
+ "cmQTL_val1_tissue_lin_PCA.jpg"
+ ),
width = 183,
height = 100,
units = "mm",
@@ -619,9 +610,9 @@ pca_plot %>%
ylab(str_c("PC2 ", "(", exp_var$PC2[[2]]*100, "%)")) +
xlab(str_c("PC1 ", "(", exp_var$PC1[[2]]*100, "%)"))
-ggsave(str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),
- "cmQTL_val1_treatment_PCA.jpg",
- sep = "_"),
+ggsave(here(out,
+ "cmQTL_val1_treatment_PCA.jpg"
+ ),
width = 183,
height = 100,
units = "mm",
@@ -665,9 +656,9 @@ pca_plot %>%
ylab(str_c("PC2 ", "(", exp_var$PC2[[2]]*100, "%)")) +
xlab(str_c("PC1 ", "(", exp_var$PC1[[2]]*100, "%)"))
-ggsave(str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),
- "cmQTL_val1_tissue_loess_PCA.jpg",
- sep = "_"),
+ggsave(here(out,
+ "cmQTL_val1_tissue_loess_PCA.jpg"
+ ),
width = 183,
height = 100,
units = "mm",
@@ -681,9 +672,9 @@ pca_plot %>%
ylab(str_c("PC2 ", "(", exp_var$PC2[[2]]*100, "%)")) +
xlab(str_c("PC1 ", "(", exp_var$PC1[[2]]*100, "%)"))
-ggsave(str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),
- "cmQTL_val1_treatment_loess_PCA.jpg",
- sep = "_"),
+ggsave(here(out,
+ "cmQTL_val1_treatment_loess_PCA.jpg"
+ ),
width = 183,
height = 100,
units = "mm",
@@ -745,9 +736,9 @@ pca_plot %>%
ylab(str_c("PC2 ", "(", exp_var$PC2[[2]]*100, "%)")) +
xlab(str_c("PC1 ", "(", exp_var$PC1[[2]]*100, "%)"))
-ggsave(str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),
- "cmQTL_val1_treatment_loess_outlier_exp2_loess_norm_PCA.jpg",
- sep = "_"),
+ggsave(here(out,
+ "cmQTL_val1_treatment_loess_outlier_exp2_loess_norm_PCA.jpg"
+ ),
width = 183,
height = 100,
units = "mm",
@@ -795,9 +786,9 @@ for(tiss in seq_along(tissues)){
ylab(str_c("PC2 ", "(", exp_var$PC2[[2]]*100, "%)")) +
xlab(str_c("PC1 ", "(", exp_var$PC1[[2]]*100, "%)"))
- ggsave(str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),
- "cmQTL_val1", tissues[[tiss]], "treatment_loess_PCA.jpg",
- sep = "_"),
+ ggsave(here(out,
+ "cmQTL_val1", tissues[[tiss]], "treatment_loess_PCA.jpg"
+ ),
width = 183,
height = 100,
units = "mm",
@@ -847,9 +838,9 @@ pca_plot %>%
ylab(str_c("PC2 ", "(", exp_var$PC2[[2]]*100, "%)")) +
xlab(str_c("PC1 ", "(", exp_var$PC1[[2]]*100, "%)"))
-ggsave(str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),
- "cmQTL_val1_tissue_imp_PCA.jpg",
- sep = "_"),
+ggsave(here(out,
+ "cmQTL_val1_tissue_imp_PCA.jpg"
+ ),
width = 183,
height = 100,
units = "mm",
@@ -867,9 +858,9 @@ pca_plot %>%
ylab(str_c("PC2 ", "(", exp_var$PC2[[2]]*100, "%)")) +
xlab(str_c("PC1 ", "(", exp_var$PC1[[2]]*100, "%)"))
-ggsave(str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),
- "cmQTL_val1_batch_imp_PCA.jpg",
- sep = "_"),
+ggsave(here(out,
+ "cmQTL_val1_batch_imp_PCA.jpg"
+ ),
width = 183,
height = 100,
units = "mm",
@@ -888,9 +879,9 @@ pca_plot %>%
ylab(str_c("PC2 ", "(", exp_var$PC2[[2]]*100, "%)")) +
xlab(str_c("PC1 ", "(", exp_var$PC1[[2]]*100, "%)"))
-ggsave(str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),
- "cmQTL_val1_class_imp_PCA.jpg",
- sep = "_"),
+ggsave(here(out,
+ "cmQTL_val1_class_imp_PCA.jpg"
+ ),
width = 183,
height = 100,
units = "mm",
@@ -937,9 +928,9 @@ pca_plot %>%
ylab(str_c("PC2 ", "(", exp_var$PC2[[2]]*100, "%)")) +
xlab(str_c("PC1 ", "(", exp_var$PC1[[2]]*100, "%)"))
-ggsave(str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),
- "cmQTL_val2_class_isnorm_PCA.jpg",
- sep = "_"),
+ggsave(here(out,
+ "cmQTL_val2_class_isnorm_PCA.jpg"
+ ),
width = 183,
height = 100,
units = "mm",
@@ -975,7 +966,7 @@ for (meta in seq_along(plotmets)) {
}
-pdf(file = str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),"_loess_fit.pdf"))
+pdf(file = here(out,"_loess_fit.pdf"))
for (meta in seq_along(plotmets)) {
@@ -1001,7 +992,7 @@ for (meta in seq_along(plotmets)) {
}
-pdf(file = str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),"_loess_norm_fw_log.pdf"))
+pdf(file = here(out,"_loess_norm_fw_log.pdf"))
for (meta in seq_along(plotmets)) {
@@ -1027,7 +1018,7 @@ for (meta in seq_along(plotmets)) {
}
-pdf(file = str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),"_loess_norm_no_scale.pdf"),
+pdf(file = here(out,"_loess_norm_no_scale.pdf"),
height = 3.5)
@@ -1053,7 +1044,7 @@ for (meta in seq_along(plotmets)) {
}
-pdf(file = str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),"_linnorm.pdf"))
+pdf(file = here(out,"_linnorm.pdf"))
for (meta in seq_along(plotmets)) {
print(plot_out[[meta]])
@@ -1093,24 +1084,24 @@ features_out <- features_all %>%
write_csv(features_out,
- str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),
- "cmQTL_val_1_2_feat_dat_GC.csv",
- sep = "_"))
+ here(out,
+ "cmQTL_val_1_2_feat_dat_GC.csv"
+ ))
write_csv(met_dat,
- str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),
- "cmQTL_val_1_2_met_dat_GC.csv",
- sep = "_"))
+ here(out,
+ "cmQTL_val_1_2_met_dat_GC.csv"
+ ))
write_csv(sam_dat,
- str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),
- "cmQTL_val_1_2_sam_dat_GC.csv",
- sep = "_"))
+ here(out,
+ "cmQTL_val_1_2_sam_dat_GC.csv"
+ ))
write_csv(missingness,
- str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),
- "cmQTL_val_1_2_miss_GC.csv",
- sep = "_"))
+ here(out,
+ "cmQTL_val_1_2_miss_GC.csv"
+ ))
# Log used code ------------------------------------------------------------