Description Usage Arguments Note Author(s)
It plots the level of gene expression of a particular gene within the plot you want.
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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. |
The code where boxplot=TRUE is adapted from Ximena Ibarra-Soria.
Blanca Pijuan-Sala.
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