plotGeneLevels: Plot gene expression

Description Usage Arguments Note Author(s)

View source: R/function_plotGeneLevels.R

Description

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

Usage

1
2
3
plotGeneLevels(data, x, y, gene, cols = c("blue", "gold"),
  pointSize = 1, xlab = "x", ylab = "y", titlePlot = gene,
  clusters = NULL, boxplot = FALSE)

Arguments

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.

Note

The code where boxplot=TRUE is adapted from Ximena Ibarra-Soria.

Author(s)

Blanca Pijuan-Sala.


BPijuanSala/anSeq documentation built on Oct. 10, 2018, 7:20 p.m.