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

Description

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

Usage

gene.plot(
  x = NULL,
  gene = NULL,
  cond.shape = FALSE,
  conds.to.plot = NULL,
  data.type = "main",
  box.to.test = 0,
  box.pval = "sig.signs",
  plot.data.type = "tsne",
  scaleValue = TRUE,
  min.scale = 0,
  max.scale = 2.5,
  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 = 1,
  box.transparency = 0.5,
  interactive = TRUE,
  out.name = "plot",
  write.data = FALSE
)

Value

An object of class iCellR.

Arguments

x: An object of class iCellR.
gene: Gene name/names to be plotted.
cond.shape: If TRUE the conditions will be shown in shapes.
conds.to.plot: Choose the conditions you want to see in the plot, default = NULL (all conditions).
data.type: Choose from "main", "atac, "atac.imputed" and "imputed", default = "main".
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, default = 0.
box.pval: Choose from "sig.values" and "sig.signs". If set to "sig.signs" p values would be replaced with signs ("na", "*", "**", "***"), default = "sig.signs".
plot.data.type: Choose between "tsne", "pca", "umap", "knetl", "diffusion", "pseudo.A" and "pseudo.B", default = "tsne".
scaleValue: Scale the colors, default = FALSE.
min.scale: If scaleValue = TRUE, set a number for min, default = -2.5.
max.scale: If scaleValue = TRUE, set a number for max, default = 2.5.
clust.dim: 2 for 2D plots and 3 for 3D plots, default = 2.
col.by: Choose from "clusters" and "conditions", default = "clusters".
plot.type: Choose from "scatterplot", "boxplot" and "barplot", default = "scatterplot".
cell.size: A number for the size of the points in the plot, default = 1.
cell.colors: Colors for heat mapping the points in "scatterplot", default = c("gray","red").
box.cell.col: A color for the points in the box plot, default = "black".
box.color: A color for the boxes in the "boxplot", default = "red".
box.line.col: A color for the lines around the "boxplot", default = "green".
back.col: A color for the plot background, default = "black".
cell.transparency: Color transparency for points in "scatterplot" and "boxplot", default = 1.
box.transparency: Color transparency for box in "boxplot", default = 0.5.
interactive: If set to TRUE an interactive HTML file will be created, default = TRUE.
out.name: If "interactive" is set to TRUE, the out put name for HTML, default = "plot".
write.data: Write export the data used for the plot plot, default = TFALSE.