## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = FALSE) ## ----style, echo=FALSE, results='asis'---------------------------------------- BiocStyle::markdown() ## ----echo = TRUE, eval = FALSE------------------------------------------------ # library("SmartPhos") # runSmartPhos() ## ----echo = TRUE, eval = FALSE------------------------------------------------ # library("SmartPhos") # makeSmartPhosDirectory(path = "shinyApp") ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "firstLook.png")) ## ----out.width = "400px"------------------------------------------------------ knitr::include_graphics(file.path("images", "preprocess1.png")) ## ----out.width = "600px"------------------------------------------------------ knitr::include_graphics(file.path("images", "preprocess2.png")) ## ----out.width = "350px"------------------------------------------------------ knitr::include_graphics(file.path("images", "preprocess3.png")) ## ----out.width = "350px"------------------------------------------------------ knitr::include_graphics(file.path("images", "preprocess4.png")) ## ----out.width = "350px"------------------------------------------------------ knitr::include_graphics(file.path("images", "error1.png")) ## ----out.width = "350px"------------------------------------------------------ knitr::include_graphics(file.path("images", "error2.png")) ## ----out.width = "350px"------------------------------------------------------ knitr::include_graphics(file.path("images", "error3.png")) ## ----out.width="400px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "preprocess.png")) ## ----out.width="300px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "otherOptions1.png")) ## ----out.width="600px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "otherOptions2.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(c(file.path("images", "boxPlot.png"), file.path("images", "logRatio.png") , file.path("images", "table.png"), file.path("images", "completeness.png"))) ## ----out.width="300px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "pca1.png")) ## ----out.width="300px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "pca2.png")) ## ----out.width="490px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "pca3.png")) ## ----out.width="600px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "pca4.png")) ## ----out.width="600px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "pca5.png")) ## ----out.width="500px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "heatmap.png")) ## ----out.width="300px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "heatmapPDF.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(c(file.path("images", "heatmap1.png"), file.path("images", "heatmap2.png"))) ## ----out.width="400px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "errorHeatmap.png")) ## ----out.width="350px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "diff_option1.png")) ## ----out.width="350px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "diff_option2.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "diff.png")) ## ----out.width="300px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "diff_filter.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "diff_click.png")) ## ----out.width="400px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "errorDEA.png")) ## ----out.width="350px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "timeSeriesOptions.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "timeSeriesClust1.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "timeSeriesClust2.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "time_series_result2.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "time_series_result3.png")) ## ----out.width="300px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "clustering0.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "clustering1.png")) knitr::include_graphics(file.path("images", "clustering2.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "timeSeriesErr1.png")) ## ----out.width="350px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "enrich_option.png")) ## ----out.width="300px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "enrich_err1.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "enrich_result1.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "enrich_resultTS.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "enrich_result1_Phospho.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "enrich_result2_Phospho.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "enrich_result2.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "enrich_result3.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "enrich_result4.png")) knitr::include_graphics(file.path("images", "enrich_result5.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "enrich_result6.png")) knitr::include_graphics(file.path("images", "enrich_result7.png")) ## ----out.width="300px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "kinase_settings1.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "kinase_result1.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "kinase_result2.png")) ## ----out.width="300px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "kinase_settings2.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "kinase_result3.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "kinase_result4.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "kinase_result5.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "kinase_err1.png")) ## ----out.width="300px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "kinase_settings3.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "kinase_result6.png")) ## ----out.width="300px"-------------------------------------------------------- knitr::include_graphics(file.path("images", "kinase_result7.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "kinase_result8.png")) ## ----------------------------------------------------------------------------- knitr::include_graphics(file.path("images", "log_info.png")) ## ----------------------------------------------------------------------------- sessionInfo()