## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE, fig.wide=TRUE) ## ----eval=FALSE--------------------------------------------------------------- # if (!require("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("signifinder") ## ----message=FALSE------------------------------------------------------------ # loading packages library(SummarizedExperiment) library(signifinder) library(dplyr) data(ovse) ovse ## ----------------------------------------------------------------------------- availSigns <- availableSignatures() ## ----echo=FALSE--------------------------------------------------------------- knitr::kable(t(availSigns[1,])) ## ----------------------------------------------------------------------------- ovary_signatures <- availableSignatures(tissue = "ovary", description = FALSE) ## ----echo=FALSE--------------------------------------------------------------- knitr::kable( ovary_signatures, caption = 'Signatures developed for ovary collected in signifinder.') %>% kableExtra::kable_paper() %>% kableExtra::scroll_box(width = "81%", height = "870px") ## ----------------------------------------------------------------------------- ovse <- ferroptosisSign(dataset = ovse, inputType = "rnaseq") ## ----------------------------------------------------------------------------- ovse <- EMTSign(dataset = ovse, inputType = "rnaseq", author = "Miow") ## ----------------------------------------------------------------------------- ovse <- multipleSign(dataset = ovse, inputType = "rnaseq", tissue = c("ovary", "pan-tissue")) ## ----fig.width=12------------------------------------------------------------- evaluationSignPlot(data = ovse) ## ----fig.wide=FALSE----------------------------------------------------------- oneSignPlot(data = ovse, whichSign = "Hypoxia_Buffa") ## ----fig.height=3, fig.wide=FALSE--------------------------------------------- geneHeatmapSignPlot(data = ovse, whichSign = "LipidMetabolism_Zheng", logCount = TRUE) ## ----------------------------------------------------------------------------- geneHeatmapSignPlot(data = ovse, whichSign = c("IFN_Ayers", "Tinflam_Ayers"), logCount = TRUE) ## ----------------------------------------------------------------------------- sign_cor <- correlationSignPlot(data = ovse) highest_correlated <- unique(unlist( sign_cor$data[(sign_cor$data$cor>0.95 & sign_cor$data$cor<1),c(1,2)] )) ## ----fig.height=9, fig.wide=FALSE--------------------------------------------- heatmapSignPlot(data = ovse) ## ----fig.height=2.5, fig.wide=FALSE------------------------------------------- heatmapSignPlot(data = ovse, whichSign = highest_correlated) ## ----fig.height=10------------------------------------------------------------ heatmapSignPlot(data = ovse, clusterBySign = paste0("ConsensusOV_Chen_", c("IMR","DIF","PRO","MES")), sampleAnnot = ovse$OV_subtype, signAnnot = "topic") ## ----------------------------------------------------------------------------- mysurvData <- cbind(ovse$os, ovse$status) rownames(mysurvData) <- rownames(colData(ovse)) head(mysurvData) ## ----------------------------------------------------------------------------- survivalSignPlot(data = ovse, survData = mysurvData, whichSign = "Pyroptosis_Ye", cutpoint = "optimal") ## ----------------------------------------------------------------------------- ridgelineSignPlot(data = ovse, whichSign = highest_correlated) ridgelineSignPlot(data = ovse, whichSign = highest_correlated, groupByAnnot = ovse$OV_subtype) ## ----echo=FALSE, out.width = "100%"------------------------------------------- knitr::include_graphics("figures/vignette_sc.png") # ## ----echo=FALSE, fig.wide=FALSE----------------------------------------------- knitr::include_graphics("figures/vignette_st.png") # ## ----------------------------------------------------------------------------- sessionInfo()