Nothing
## ----setup, include = FALSE, echo = FALSE-------------------------------------
knitr::opts_chunk$set(echo = TRUE,
warning = FALSE,
message = FALSE,
fig.height = 7,
fig.width=7,
fig.align = "center")
library(knitr)
library(kableExtra)
## ---- echo=FALSE--------------------------------------------------------------
library(ggplot2)
library(ggpubr)
library(plotly)
library(usethis)
## ---- eval=FALSE--------------------------------------------------------------
# library(volcano3D)
#
# # Basic DESeq2 set up
# library(DESeq2)
#
# counts <- matrix(rnbinom(n=3000, mu=100, size=1/0.5), ncol=30)
# rownames(counts) <- paste0("gene", 1:100)
# cond <- rep(factor(rep(1:3, each=5), labels = c('A', 'B', 'C')), 2)
# resp <- factor(rep(1:2, each=15), labels = c('non.responder', 'responder'))
# metadata <- data.frame(drug = cond, response = resp)
#
# # Full dataset object construction
# dds <- DESeqDataSetFromMatrix(counts, metadata, ~response)
#
# # Perform 3x DESeq2 analyses comparing binary response for each drug
# res <- deseq_2x3(dds, ~response, "drug")
## ---- eval=FALSE--------------------------------------------------------------
# library(easylabel)
# df <- as.data.frame(res[[1]]) # results for the first drug
# easyVolcano(df)
## ---- eval=FALSE--------------------------------------------------------------
# # Generate polar object
# obj <- deseq_2x3_polar(res)
#
# # 2d plot
# radial_plotly(obj)
#
# # 3d plot
# volcano3D(obj)
## ---- eval=FALSE--------------------------------------------------------------
# obj <- deseq_2x3_polar(data1)
# labs <- c('MS4A1', 'TNXA', 'FLG2', 'MYBPC1')
# radial_plotly(obj, type=2, label_rows = labs) %>% toWebGL()
## ----radial_2x3_pos, echo = FALSE, message=FALSE, fig.align='center', out.width='70%', out.extra='style="border: 0;"'----
knitr::include_graphics("radial_2x3_pos.png")
## ----volc_2x3, echo = FALSE, message=FALSE, fig.align='center', out.width='70%', out.extra='style="border: 0;"'----
knitr::include_graphics("volc3d_2x3.png")
## ---- eval=FALSE--------------------------------------------------------------
# obj <- deseq_2x3_polar(data1, process = "negative")
# labs <- c('MS4A1', 'TNXA', 'FLG2', 'MYBPC1')
# radial_plotly(obj, type=2, label_rows = labs) %>% toWebGL()
## ----radial_2x3_neg, echo = FALSE, message=FALSE, fig.align='center', out.width='70%', out.extra='style="border: 0;"'----
knitr::include_graphics("radial_2x3_neg.png")
## ----eval=FALSE---------------------------------------------------------------
# polar_obj <- polar_coords_2x3(vstdata, metadata, "ACR.response.status",
# "Randomised.Medication")
#
# radial_plotly(polar_obj, type=2)
# volcano3D(polar_obj)
## ---- eval=FALSE--------------------------------------------------------------
# forest_ggplot(obj, c("MS4A1", "FLG2", "SFN")
## ----forest, echo = FALSE, message=FALSE, fig.align='center', out.width='70%', out.extra='style="border: 0;"'----
knitr::include_graphics("forest.png")
## -----------------------------------------------------------------------------
citation("volcano3D")
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