Merge branch 'release/0.7.1'

README.md

@@ -1,6 +1,6 @@
 <!-- # DOOMSAYER -->
 
-![](assets/doomsayer_logo2.png)
+![](https://raw.githubusercontent.com/carjed/doomsayer/master/assets/doomsayer_logo2.png)
 
 [![DOI](https://zenodo.org/badge/95728792.svg?style=flat)](https://zenodo.org/badge/latestdoi/95728792) [![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](http://www.jedidiahcarlson.com/docs/doomsayer) [![License: MIT](https://img.shields.io/badge/license-MIT-blue.svg?style=flat)](https://opensource.org/licenses/MIT)  [![Binder](https://img.shields.io/badge/launch-binder-d06681.svg?style=flat)](https://mybinder.org/v2/gh/carjed/doomsayer/master) [![Build Status](https://travis-ci.org/carjed/doomsayer.svg?style=flat?branch=master)](https://travis-ci.org/carjed/doomsayer)
 

mkdocs.yml

@@ -3,6 +3,7 @@ site_url: https://github.com/carjed/doomsayer
 repo_url: https://github.com/carjed/doomsayer
 pages:
   - Home: index.md
+  - Usage: usage.md
   - FAQ: faq.md
   - Support: support.md
 theme: cinder

report_templates/R/stat_boxplots1.Rmd

@@ -0,0 +1,52 @@
+```{r boxplots1, results='asis', message=FALSE, warning=FALSE, echo=FALSE, fig.height = 8, fig.width = 12, dpi=100,  fig.align="center"}
+
+if(exists("samples") & exists("svars")){
+
+  cat("## Outlier QC statistic boxplots \n")
+
+  cat("### Plot description \n")
+
+  cat("If the user has included a file of sample-level summary statistics with the --samplefile` option and has specified variables to analyze with the `--svars` option, this plot will show the distributions of those variables for the outliers compared to the inlier samples. \n \n")
+
+  cat("### Interpreting this plot \n")
+
+  cat("These boxplots tell us whether the outliers detected by *Doomsayer* show differences in other sample-level summary statistics. \n")
+
+  sigs2 <- merge(sig_contribs, samples, by="ID") %>%
+    mutate(outlier=ifelse(ID %in% outlier_IDs, T, F))
+  
+  sigs2 <- merge(sigs2, cluster_mems, by="ID", all.x=T)
+  sigs2[is.na(sigs2$group),]$group <- "keep"
+
+  sumdat <- sigs2 %>%
+    # filter(sig!=2) %>%
+    group_by(group) %>%
+    dplyr::select(c("ID","group",svars)) %>%
+    # filter(coverage < 15) %>%
+    gather(var, val, svars[1]:svars[length(svars)]) %>%
+    group_by(group, var)
+  
+  # figure showing that simple cutoffs for quality indicators would not easily
+  # differentiate inliers vs. Doomsayer's flagged outliers
+  sumdat1 <- sumdat %>%
+    ungroup() %>%
+    mutate(group = gsub(" .*", "", group))
+  
+  p1 <- ggplot(sumdat1, aes(x=group, y=val, group=group, fill=group))+
+    geom_boxplot()+
+    scale_fill_manual(values=c("gray30", "red"))+
+    facet_wrap(~var, scales="free")+
+    theme_bw()+
+    theme(axis.text.x=element_text(angle=45, hjust=1),
+      axis.title.x=element_blank(),
+      legend.position="none")
+    
+  sggplotly(p1)
+
+} else {
+  sigs2 <- merge(sig_contribs, cluster_mems, by="ID", all.x=T) %>%
+    mutate(outlier=ifelse(ID %in% outlier_IDs, T, F))
+  sigs2[is.na(sigs2$group),]$group <- "keep"
+}
+
+```

report_templates/R/stat_boxplots2.Rmd

@@ -0,0 +1,28 @@
+```{r boxplots2, results='asis', message=FALSE, warning=FALSE, echo=FALSE, fig.height = 8, fig.width = 12, dpi=100,  fig.align="center"}
+
+if(exists("samples") & exists("svars")){
+
+  cat("### Plot description \n")
+
+  cat("The plot below shows the distributions of user-specified QC variables for the inlier samples compared to the outlier samples grouped according to the cluster assignment shown in the [heatmap](#error_profile_heatmap) \n \n")
+
+  cat("### Interpreting this plot \n")
+
+  cat("These boxplots tell us whether **specific groups** of outliers detected by *Doomsayer* show differences in other sample-level summary statistics. \n")
+
+  # figure showing that simple cutoffs for quality indicators would not easily
+  # differentiate inliers vs. Doomsayer's flagged outliers
+  p2 <- ggplot(sumdat, aes(x=group, y=val, group=group, fill=group))+
+    geom_boxplot()+
+    scale_fill_manual(values=c("gray30", group_col_vals))+
+    facet_wrap(~var, scales="free")+
+    theme_bw()+
+    theme(axis.text.x=element_text(angle=45, hjust=1),
+      axis.title.x=element_blank(),
+      legend.position="none")
+    
+  sggplotly(p2)
+  
+} 
+
+```

report_templates/diagnostics.Rmd

@@ -43,13 +43,10 @@ Note that a lack of obvious clustering patterns does not necessarily mean the fl
 ```{r child="R/heatmap.Rmd"}
 ```
 
-## Outlier QC statistic boxplots
-
-### Plot description
-
-If the user has included a file of sample-level summary statistics with the `--samplefile` option and has specified variables to analyze with the `--svars` option, this plot will show the distributions of those variables for the outliers in each cluster, compared to the inlier samples.
+```{r child="R/stat_boxplots1.Rmd"}
+```
 
-```{r child="R/stat_boxplots.Rmd"}
+```{r child="R/stat_boxplots2.Rmd"}
 ```
 
 ## Compare component distributions
@@ -77,7 +74,7 @@ If you are using NMF decomposition and two or more components are perfectly corr
 
 ### Plot description
 
-Each bar represents the fraction of observations contained within that K-mer subtype across all samples of a particular group. 
+Each bar represents the fraction of observations contained within that K-mer subtype across all samples of a particular group. Bars that are solid colors indicate the outliers in that group have a significantly higher or lower proportion of those SNVs compared to the inlier group (FDR-adjusted; Q-value < 0.05), whereas greyed-out bars indicate no significant difference.
 
 ```{r child="R/spectra.Rmd"}
 ```