Merge pull request #3 from LiChenPU/dev

Dev
LiChenPU · Sep 15, 2021 · 9f63202 · 9f63202
2 parents 225960d + e522e9c
commit 9f63202
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Showing 19 changed files with 21,763 additions and 3,978 deletions.
diff --git a/FDR_example/Target-Decoy Generator.R b/FDR_example/Target-Decoy Generator.R
@@ -209,7 +209,7 @@ FDR_Calculator <- function(decoy_address, output_address,
     anns_elements <- sapply(anns, function(x) unlist(strsplit(x, "\\d+")))
     decoys <- sapply(anns_elements, function(x) sum(unlist(x) %in% imp_elements))
     FP <- length(which(decoys > 0)) * (f - 1)
-    FDR <- FP / (length(anns) - FP)
+    FDR <- FP / (length(anns))
 }
 
 NetID <- function(work_dir, file_name, ion_mode, decoy_lib) {

diff --git a/FDR_example/plot.R b/FDR_example/plot.R
@@ -51,7 +51,7 @@ load("FDR.RData")
   ## Plot ####
   {
     p_all_precision = ggplot(data = gt_all, mapping = aes(x = method, y = precision, color = method)) + 
-      geom_boxplot() + #geom_point(data = stan, mapping = aes(x = method, y = precision, fill = method), shape = 22, color = "black") +
+      geom_boxplot(outlier.shape = NA) + #geom_point(data = stan, mapping = aes(x = method, y = precision, fill = method), shape = 22, color = "black") +
       geom_point(alpha = 1 / 5, position = "jitter") +
       # ggtitle("Precision by Ground Truth") + 
       theme_classic(base_size = 12 # edit font size for all non-data text
@@ -76,7 +76,7 @@ load("FDR.RData")
       facet_wrap(~ library, nrow = 2) #+coord_flip()
 
     p1_precision = ggplot(data = gt_all %>% filter(library=="HMDB"), mapping = aes(x = method, y = precision, color = method)) + 
-      geom_boxplot() + #geom_point(data = stan, mapping = aes(x = method, y = precision, fill = method), shape = 22, color = "black") +
+      geom_boxplot(outlier.shape = NA) + #geom_point(data = stan, mapping = aes(x = method, y = precision, fill = method), shape = 22, color = "black") +
       geom_point(alpha = 1 / 5, position = "jitter") +
       # ggtitle("Precision by Ground Truth") +
       # guides(color = F) +
@@ -147,7 +147,7 @@ load("FDR.RData")
   ## Plot ####
   {
     p_all_FDR = ggplot(data = fdr_all, mapping = aes(x = method, y = FDR, color = method)) + 
-      geom_boxplot() + #geom_point(data = stan, mapping = aes(x = method, y = precision, fill = method), shape = 22, color = "black") +
+      geom_boxplot(outlier.shape = NA) + #geom_point(data = stan, mapping = aes(x = method, y = precision, fill = method), shape = 22, color = "black") +
       geom_point(alpha = 1 / 5, position = "jitter") +
       # ggtitle("Precision by Ground Truth") + 
       theme_classic(base_size = 12 # edit font size for all non-data text
@@ -172,7 +172,7 @@ load("FDR.RData")
       facet_wrap(~ library, nrow = 2) #+coord_flip()
 
     p1_FDR = ggplot(data = fdr_all %>% filter(library=="HMDB"), mapping = aes(x = method, y = FDR, color = method)) + 
-      geom_boxplot() + #geom_point(data = stan, mapping = aes(x = method, y = precision, fill = method), shape = 22, color = "black") +
+      geom_boxplot(outlier.shape = NA) + #geom_point(data = stan, mapping = aes(x = method, y = precision, fill = method), shape = 22, color = "black") +
       geom_point(alpha = 1 / 5, position = "jitter") +
       # ggtitle("Precision by Ground Truth") + 
       guides(color = guide_legend(

diff --git a/FDR_example/plot_7_1.pdf b/FDR_example/plot_7_1.pdf
diff --git a/FDR_example/plot_7_1_all.pdf b/FDR_example/plot_7_1_all.pdf
diff --git a/FDR_example/plot_7_2.pdf b/FDR_example/plot_7_2.pdf
diff --git a/FDR_example/plot_7_2_all.pdf b/FDR_example/plot_7_2_all.pdf
diff --git a/FDR_example/plot_merge.pdf b/FDR_example/plot_merge.pdf
diff --git a/NetID_statistics/summary.xlsx b/NetID_statistics/summary.xlsx
diff --git a/Sc_neg/NetID_output.csv b/Sc_neg/NetID_output.csv
diff --git a/Sc_neg/cyto_edges.csv b/Sc_neg/cyto_edges.csv
diff --git a/Sc_neg/cyto_nodes.csv b/Sc_neg/cyto_nodes.csv
diff --git a/get started/UserGuideMD/UG.html b/get started/UserGuideMD/UG.html
diff --git a/get started/UserGuideMD/UG.log b/get started/UserGuideMD/UG.log