plotGeneLevels: Plot gene expression
In BPijuanSala/anSeq: Tools to analyse RNA-seq data

Description Usage Arguments Note Author(s)

It plots the level of gene expression of a particular gene within the plot you want.

1
2
3

plotGeneLevels(data, x, y, gene, cols = c("blue", "gold"),
  pointSize = 1, xlab = "x", ylab = "y", titlePlot = gene,
  clusters = NULL, boxplot = FALSE)

`data`	Dataframe or matrix containing the counts (genes x cells). The cells should correspond to the ones used for the plot. This matrix is only used to take the values of the row of the gene to plot.
`x`	x coordinate. It needs to have entries per each cell in the counts matrix. e.g. tsne$Y[,1] when performing tSNE on those cells.The plot does not need to be based all genes.
`y`	y coordinate. It needs to have entries per each cell in the counts matrix. e.g. tsne$Y[,2] when performing tSNE on those cells.The plot does not need to be based all genes.
`gene`	Gene that you want the expression of. This should be the row ID in your data table.
`cols`	Colour range for the expression values. Default: blue,gold.
`pointSize`	cex size for points. Default: 1.
`xlab`	x-label. Default: "x".
`ylab`	y-label. Default: "y".
`titlePlot`	plot title. Default: the gene name introduced in "gene".
`clusters`	If boxplot=TRUE, this should be specified. It should be a vector of cells as names and colors defining the cluster the cell belongs to. The colours will be used for colouring the boxplots.
`boxplot`	Logical. TRUE: It will plot a boxplot next to it with the gene expression levels per cluster.