geneScatters: Scatter plot for the expression of a gene for two datasets...
In barzine/barzinePhdR: Code developed while and for my PhD thesis at the EMBL-EBI

geneScatters

R Documentation

Scatter plot for the expression of a gene for two datasets across different tissues

Description

Scatter plot for the expression of a gene for two datasets across different tissues

Usage

geneScatters(ID, DF1, DF2, palette, nameIt = TRUE,
  mapID = barzinePhdData::gene.mapID, logIt = TRUE,
  label.DF1 = "Uhlén et al. (mRNA)\nlog2(FPKM+1)",
  label.DF2 = "Pandey lab (protein)\nlog2(PPKM+1)", xcoord, ycoord,
  colNamesDF1 = c("Tissue", "Transcriptomics"),
  colNamesDF2 = c(colNamesDF1[1], "Proteomics"), base_size = 11,
  base_family = "Linux Libertine", label_size = 3.4,
  label_family = base_family, centerTitle = TRUE,
  useCor = "everything")

Arguments

`ID`	character string, gene identifier
`DF1`	numeric data.frame or equivalent
`DF2`	numeric data.frame or equivalent
`palette`	named character vector with the colour hex code to use
`nameIt`	logical, default TRUE. Whether the gene name (from mapID) should be incorporated to the plot title
`mapID`	named character vector. Map the gene identifiers to their name. default: `gene.mapID`
`logIt`	logical, default TRUE. Whether the data should be log2 transform before plotting
`label.DF1`	character string for DF1 labelling. Used as x-axis title
`label.DF2`	character string for DF2 labelling. Used as y-axis title
`xcoord`	vector of two numeric. Gives the min and max of the x-axis
`ycoord`	vector of two numeric. Gives the min and max of the y-axis
`colNamesDF1`	default: c('Tissue','Transcriptomics')
`colNamesDF2`	default: c('Tissue','Proteomics')
`base_size`	numeric, default: 11
`base_family`	default: Linux Libertine
`label_size`	numeric, default 3.4
`label_family`	default: same as base_family
`centerTitle`	logical, default TRUE
`useCor`	default: 'everything' an optional character string for 'cor' which gives a method for computing covariances in the presence of missing values. This must be (an abbreviation of) one of the strings "everything", "all.obs", "complete.obs", "na.or.complete", or "pairwise.complete.obs".