New version 0.3.0

nunofonseca · Oct 19, 2020 · c120169 · c120169
1 parent b389ebe
commit c120169
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Showing 3 changed files with 17 additions and 18 deletions.
diff --git a/scripts/msi b/scripts/msi
@@ -19,7 +19,7 @@
 #
 # =========================================================
 
-MSI_VERSION="0.2.11"
+MSI_VERSION="0.3.0"
 PATH2SCRIPT=$(dirname "${BASH_SOURCE[0]}" )
 ## load shell functions
 source $PATH2SCRIPT/msi_shared.sh

diff --git a/scripts/msi_install.sh b/scripts/msi_install.sh
@@ -322,7 +322,7 @@ function install_all {
 }
 
 function msi_to_docker {
- MSI_VERSION="0.2.11"
+ MSI_VERSION="0.3.0"
  set -e
  echo "Generating docker image with MSI...this may take a while"
  pushd $PATH2SCRIPT/..

diff --git a/template/dashboard.Rmd b/template/dashboard.Rmd
@@ -195,13 +195,13 @@ Row
 -----------------------------------------------------------------------
 
 ### Initial data {data-width=700}
-```{r}
-DT::datatable(all.data[,-c(21)], 
- options = list(
- autoWidth = TRUE,
- bPaginate = TRUE
-))
-```
+#```{r}
+#DT::datatable(all.data[,-c(21)], 
+# options = list(
+# autoWidth = TRUE,
+# bPaginate = TRUE
+#))
+#```
 
 
 Summary results
@@ -671,8 +671,8 @@ Row
 ### Top X hits per sample (heatmap)
 
 ```{r, fig.height=8}
-library(d3heatmap)
-renderD3heatmap({
+library(heatmaply)
+renderPlotly({
  x<-get.top.id.species.matrix()
  #head(dd)
  #x<-dd
@@ -684,7 +684,7 @@ renderD3heatmap({
  x<-x[,-c(1,2,3,4,5,6),drop=FALSE]
  print(head(x))
  print(typeof(x))
- d3heatmap(x,colors = colors,xaxis_font_size="10pt")
+ heatmaply(x,colors = colors,xaxis_font_size="10pt")
  ##scale = "column")
 })
 ```
@@ -696,8 +696,8 @@ Row
 ### Sample level correlation
 
 ```{r, fig.height=8}
-library(d3heatmap)
-renderD3heatmap({
+library(heatmaply)
+renderPlotly({
  x<-get.top.id.species.matrix()
  rownames(x)<-x$species
  colfunc <- colorRampPalette(c("lightgray","darkblue"))
@@ -706,7 +706,7 @@ renderD3heatmap({
 
  x<-x[,-c(1,2,3,4,5,6),drop=FALSE]
  xc<-cor(x,method="spearman")
- p<-d3heatmap(xc,colors = colors,xaxis_font_size="10pt")
+ p<-heatmaply(xc,colors = colors,xaxis_font_size="10pt")
  p
  ##scale = "column")
 })
@@ -741,7 +741,6 @@ renderPlot({
  
 renderPlot({
  
-
  x<-get.top.id.species.matrix()
  suppressPackageStartupMessages(library("gplots"))
 #install.packages("gplots")
@@ -753,10 +752,10 @@ renderPlot({
  rownames(x2)<-x$species
  x2<-x2[,-c(1,2,3),drop=FALSE]
  xc<-cor(x2,method="spearman")
- library(d3heatmap)
+ library(heatmaply)
  #if (!require("devtools")) install.packages("devtools")
  #devtools::install_github("rstudio/d3heatmap")
- d3heatmap(as.matrix(xc), scale = "column", colors = "Spectral")
+ heatmaply(as.matrix(xc), scale = "column", colors = "Spectral")
 },height=1000,width=1000)
 ```