archive dirty local repo on 2020-09-10, commit all changes

the changes seem to be about changing a coefficients visualization
to coefficients-horizontal. might also include other things.

--HG--
branch : coefficients-horizontal

MS-analysis.R

@@ -119,6 +119,7 @@ for (primary in linked) {
 exclusions <- unique(c(linked, hcs_post_wtc, xmhc))
 novel.df <- subset(ms.df, ! (gene_symbol %in% exclusions))
 novel.df <- novel.df[order(novel.df$prediction_pre_wtc, decreasing=TRUE), ]
+sum(novel.df$prediction_pre_wtc >= 0.02430711) # novel genes exceeding prediction threshold
 nominal.novel.df <- subset(novel.df, meta_p_value <= 0.05)
 
 BonferroniValidator <- function(pvals, alpha=0.05) {

gene-set-subset.R

@@ -70,6 +70,7 @@ auroc.df$mask_type <- factor(auroc.df$mask_type, levels=c('node', 'edge'))
 
 gg.auroc <- auroc.df %>%
   dplyr::filter(! (mask_type == 'edge' & subset_kind == 'minimum')) %>%
+  dplyr::filter(! (metanode == 'tissue' & subset_kind == 'minimum')) %>%
   dplyr::left_join(msigdb.df %>% dplyr::select(metanode, metanode_name)) %>%
   ggplot(aes(x, auroc)) %>% SetGGTheme() +
   facet_wrap( ~ metanode_name, ncol = 5) +

predictions_all-diseases.R

@@ -84,28 +84,29 @@ close(predictions.file)
 coef.df$neg_ridge_zcoef <- -coef.df$ridge_zcoef
 coef.melt <- reshape2::melt(subset(coef.df, feature != 'intercept'),
   measure.vars=c('neg_ridge_zcoef', 'lasso_zcoef'))
+coef.melt$variable <- factor(coef.melt$variable, levels=c('lasso_zcoef', 'neg_ridge_zcoef'))
 
 coef.melt.ridge <- subset(coef.melt, variable=='neg_ridge_zcoef')
-coef.sorted <- coef.melt.ridge[order(coef.melt.ridge$value, decreasing=TRUE), 'name']
+coef.sorted <- coef.melt.ridge[order(coef.melt.ridge$value, decreasing=FALSE), 'name']
 
 gg.zcoef <- ggplot(coef.melt, aes(x=name, ymin=0, ymax=value, color=variable))
 gg.zcoef <- SetGGTheme(gg.zcoef) +
-  geom_linerange(stat='identity', size=4.2) + 
+  geom_linerange(stat='identity', size=4.5) + 
   geom_hline(yintercept=0, color=Solar('base02')) +
-  coord_flip() +
+  #coord_flip() +
   ylab('Standardized Coefficient') +
   scale_x_discrete(limits=coef.sorted) + 
   scale_y_continuous(labels=abs) +
-  scale_color_manual(name='Method (AUROC)', values=c(Solar('red'), Solar('blue')), 
-    labels=c(sprintf('ridge (%.3f)', vtm.ridge$auroc), 
-             sprintf('lasso (%.3f)', vtm.lasso$auroc))) +
+  scale_color_manual(name='Method (AUROC)', values=c(Solar('blue'), Solar('red')), 
+    labels=c(sprintf('lasso (%.3f)', vtm.lasso$auroc),
+             sprintf('ridge (%.3f)', vtm.ridge$auroc))) +
   theme(legend.key=element_rect(linetype='blank')) +
-  theme(axis.text.y=element_text(angle=30, hjust=1)) + xlab(NULL) +
-  theme(legend.justification=c(1,0), legend.position=c(1,0), 
+  theme(axis.text.x=element_text(angle=45, hjust=1, size=9)) + xlab(NULL) +
+  theme(legend.justification=c(1,1), legend.position=c(1,1), 
     legend.background=element_rect(color='grey60', size=0.2))
 
-path <- file.path(dirs$plots, 'coefficients.pdf')
-OpenPDF(path, width=width.half, height=4.5)
+path <- file.path(dirs$plots, 'coefficients-horizontal.pdf')
+OpenPDF(path, width=5.25, height=2.8)
 print(gg.zcoef)
 ClosePDF(path)