Commit fc8466c4 authored by Holger Brandl's avatar Holger Brandl

Merge branch 'master' of git.mpi-cbg.de:bioinfo/ngs_tools

parents e8bb79f0 68335f0c
......@@ -461,7 +461,7 @@ dge_create_explorer_app() {
# check if required files exist in the current working directory
files='tpms_by_replicate.txt fpkms_by_replicate.txt de_results.txt basic_design.txt'
ls "$files" 2>/dev/null || { echo "Can not create app, because not all required data files ($files) exist in the current directory" 1>&2; return; }
ls $files 2>/dev/null || { echo "Can not create app, because not all required data files ($files) exist in the current directory" 1>&2; return; }
appify ${NGS_TOOLS}/dge_workflow/expression_explorer/run_expression_explorer.sh
......
......@@ -7,6 +7,7 @@ export SCRIPT_DIRECTORY="$(dirname "$0")/"
#https://stackoverflow.com/questions/26465240/how-to-execute-a-shell-script-from-within-an-app-and-show-it-in-the-terminal
#osascript -e 'display notification "Starting expression explorer... Please be patient, it may require some minutes to install required dependencies on first launch'
# To use Rscript as interpreter see https://stackoverflow.com/questions/1815606/rscript-determine-path-of-the-executing-script
/usr/local/bin/Rscript -<<"EOF" ${SCRIPT_DIRECTORY}
......@@ -60,7 +61,7 @@ de_res <- read_tsv(file.path(dataPath, "de_results.txt")) %>%
transmute(external_gene_name, condition_1, condition_2, logfc = c1_over_c2_logfc, pvalue, padj, is_hit, c1_overex)
de_res[,c(4:6)] <- round(de_res[,c(4:6)], 3)
design <- read_tsv(file.path(dataPath, "basic_design.txt")) %>% select(-batch)
design <- read_tsv(file.path(dataPath, "basic_design.txt")) %>% select(condition, replicate)
fpkms <- read_tsv(file.path(dataPath, "fpkms_by_replicate.txt")) %>%
mutate(method = "fpkm") %>%
......@@ -171,7 +172,7 @@ app <- shinyApp(
plot <- ggplot(plot_data, aes(condition, rep_values, color = gene_name)) +
geom_point(position=pd) +
theme(axis.text.x = element_text(angle = 50, hjust = 1)) +
ylab(paste(input$method, "s", sep = "")) +
ylab(toupper(input$method)) +
xlab("condition")
if (is.element("plot_line", input$options)) {
......
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