The tmod Visualization Gallery

knitr::opts_chunk$set(
  echo = FALSE,
  collapse = TRUE,
  comment = "#>"
)
library(dplyr)
library(tmod)

The purpose of this document is the demonstration and explanation of the main visualizations which can be generated by tmod. In the following, we make use of tidyverse and colorDF.

tmod PanelPlots

The function tmodPanelPlot generates a heatmap-like representation combining information on gene enrichment and differential gene expression, including both a q-value and effect size for the enrichment part.

data(vaccination)
vaccination %>% 
  select(GeneName, Description, logFC.F.D1, qval.F.D1) %>%
  arrange(qval.F.D1)
days <- paste0("D", c(1:5, 7))
res <- lapply(days, function(d) {
  q <- paste0("qval.F.", d)
  l <- vaccination$GeneName[ order(vaccination[[q]]) ]
  tmodCERNOtest(l, mset="LI", qval=.1)
})

lfcs <- vaccination %>% select(starts_with("logFC"))
pvals <- vaccination %>% select(starts_with("qval"))

pie <- tmodDecideTests(vaccination$GeneName, lfc=lfcs, pval=pvals)
names(pie) <- names(res) <- days


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tmod documentation built on Oct. 23, 2020, 6:12 p.m.