gene.plot: Make scatter, box and bar plots for genes

In rezakj/scSeqR: scSeqR; a toolkit to analyze single cell sequencing data types (i.e scRNA-seq) and large numeric matrix files.

Make scatter, box and bar plots for genes

Description

This function takes an object of class scSeqR and provides plots for genes.

Usage

gene.plot(x = NULL, gene = "NULL", box.to.test = 0,
  box.pval = "sig.signs", plot.data.type = "tsne", clust.dim = 2,
  col.by = "clusters", plot.type = "scatterplot", cell.size = 1,
  cell.colors = c("gray", "red"), box.cell.col = "black",
  box.color = "red", box.line.col = "green", back.col = "white",
  cell.transparency = 0.5, interactive = TRUE, out.name = "plot")

Arguments

x	An object of class scSeqR.
gene	A gene name to be plotted.
box.to.test	A cluster number so that all the boxes in the box plot would be compared to. If set to "0" the cluster with the highest avrage would be choosen, defult = 0.
box.pval	Choose from "sig.values" and "sig.signs". If set to "sig.signs" p values would be replaced with signs ("na", "*", "**", "***"), defult = "sig.signs".
plot.data.type	Choose from "tsne" and "pca", defult = "tsne".
clust.dim	2 for 2D plots and 3 for 3D plots, defult = 2.
col.by	Choose from "clusters" and "conditions", defult = "clusters".
plot.type	Choose from "scatterplot", "boxplot" and "barplot", defult = "scatterplot".
cell.size	A number for the size of the points in the plot, defult = 1.
cell.colors	Colors for heat mapping the points in "scatterplot", defult = c("gray","red").
box.cell.col	A color for the points in the box plot, defult = "black".
box.color	A color for the boxes in the "boxplot", defult = "red".
box.line.col	A color for the lines around the "boxplot", defult = "green".
back.col	A color for the plot background, defult = "black".
cell.transparency	Color transparency for points in "scatterplot" and "boxplot", defult = 0.5.
interactive	If set to TRUE an intractive HTML file will be created, defult = TRUE.
out.name	If "interactive" is set to TRUE, the out put name for HTML, defult = "plot".

Value

An object of class scSeqR.

Examples

## Not run: 
cluster.plot(my.obj,
            cell.size = 1,
            plot.type = "tsne",
            cell.color = "black",
            back.col = "white",
            col.by = "clusters",
            cell.transparency = 0.5,
            clust.dim = 3,
            interactive = T,
            density = F,
            out.name = "tSNE_3D_clusters")

cluster.plot(my.obj, cell.size = 1,
            plot.type = "tsne",
            col.by = "clusters",
            cell.transparency = 0.5,
            clust.dim = 2,
            interactive = T,
            density = F,
            out.name = "tSNE_2D_clusters")

cluster.plot(my.obj,
           cell.size = 2,
           plot.type = "tsne",
           clust.dim = 2,
           interactive = F)

cluster.plot(my.obj,
           cell.size = 1,
           plot.type = "tsne",
           col.by = "clusters",
           clust.dim = 3,
           interactive = F,
           angle = 45)


cluster.plot(my.obj,
          cell.size = 1,
          plot.type = "pca",
          cell.color = "black",
          back.col = "white",
          col.by = "conditions",
          cell.transparency = 0.5,
          clust.dim = 3,
          interactive = T,
          density = F,
          out.name = "PCA_3D_conditions")

## End(Not run)

rezakj/scSeqR documentation built on March 28, 2022, 12:17 p.m.