report: diamond: fig w/o log10 and zoomed in (issue #22)

workflow_report/scripts/report.R

@@ -191,6 +191,7 @@ FIGS$diamond$normal <-
         axis.text.x=element_text(size=9, color="black", angle=90, vjust=0.5, hjust=1)
     )
 FIGS$diamond$log <- FIGS$diamond$normal + scale_y_continuous(trans="log10")
+FIGS$diamond$normal_zoom <- FIGS$diamond$normal + coord_cartesian(ylim=c(0, 1.5))
 
 ##############################
 # RGI: AMR prediction

workflow_report/scripts/report.Rmd

@@ -53,6 +53,7 @@ print(FIGS$prodigal$counts)
 ```
 
 ```{r figures-prodigal-pct, echo=FALSE, fig.width=10, fig.height=5}
+knitr::opts_chunk$set(warning=FALSE)
 print(FIGS$prodigal$pct)
 ```
 
@@ -62,6 +63,10 @@ print(FIGS$prodigal$pct)
 print(FIGS$diamond$log)
 ```
 
+```{r figures-diamond-zoom, echo=FALSE, fig.width=10, fig.height=5, fig.cap='nr UniProtKB/TrEMBL, zoomed in'}
+FIGS$diamond$normal_zoom
+```
+
 ## Plasmid prediction
 
 ```{r figures-plasflow, echo=FALSE, fig.width=10, fig.height=5, fig.cap='Plasmid prediction w/ Plasflow'}