Spaghetti plot for Specific Gene Set

Spaghetti plot for Specific Gene Set

Usage

spaghettiPlot1GS(
  gs_index,
  gmt,
  expr_mat,
  design,
  var_time,
  var_indiv,
  sampleIdColname,
  var_group = NULL,
  var_subgroup = NULL,
  plotChoice = c("Medians", "Individual"),
  loess_span = 0.75
)

Arguments

gs_index

index of the specific gene set in gmt.

gmt

a list of elements: geneset, geneset.name and geneset.description (see GSA.read.gmt).

expr_mat

a data.frame with numerics of size G x n contraining the raw RNA-seq counts from n samples for G genes.

design

a data.frame or DFrame containing the information of each sample (SampleID).

var_time

the time or visit variable contained in design.

var_indiv

the patient variable contained in design data.

sampleIdColname

a character string indicating the name of the sample ID variable in design to be matched with the colnames of expr_mat

var_group

a group variable in design data to divide into two facets. Default is NULL.

var_subgroup

a subgroup variable in design data to add 2 curves on plot for each subgroup. Default is NULL.

plotChoice

to choose which type of plot (either "Medians", "Individual" or both). Default is c("Medians", "Individual").

loess_span

smoothing span. Default is 0.75.

Value

a ggplot2 plot object

Examples

data(baduel_5gs) 
design$Indiv <- design$Population:design$Replicate
design$Vern <- ifelse(design$Vernalized, "Vernalized", "Non-vernalized")

library(ggplot2)
spaghettiPlot1GS(gs_index = 3, gmt = baduel_gmt, expr_mat = log2(expr_norm_corr+1), 
  design = design, var_time = AgeWeeks, var_indiv = Indiv, 
  sampleIdColname = "sample", var_group=Vern, var_subgroup=Population, 
  plotChoice = "Medians", loess_span= 1.5) +
  xlab("Age (weeks)") + guides(color= "none")