gene_grapher: gene_grapher

In atakanekiz/SCseqtools: Deal With Your Single Cell RNAseq Data With Ease

gene_grapher

Description

A function to generate gene expression plots from data frames derived from single cell RNAseq data.

Usage

gene_grapher(
  exprs,
  genes_to_plot,
  x_variable = "sample",
  clusters_to_plot = NULL,
  pos_marker = NULL,
  neg_marker = NULL,
  plot_type = "box",
  add_jitter = T,
  add_point = F,
  point_size = 0.2,
  point_alpha = 0.2,
  add_mean = T,
  mean_color = "red",
  add_median = T,
  median_color = "blue",
  sort_plots = F,
  colors_to_use = NULL,
  show_stats = T,
  comparisons = NULL,
  stat_method = "wilcox.test",
  p_adj_method = "holm",
  y_expand_low = 0,
  y_expand_high = 0.2,
  pval_y_offset = 5/6,
  save_pdf = F,
  append_to_filename = "",
  output_plot = T,
  assign_global_plotlist = F,
  show_progress = F,
  image_columns = 4,
  image_rows = 4,
  ...
)

Arguments

exprs	An expression data frame. Easily generated using HTtools::df_extractor() function. Two columns should be present named "sample", and "cluster". The other columns contain gene names and normalized expression values
genes_to_plot	Character vector of gene names
x_variable	What to show on axis. It can be "sample" (default), "cluster"
clusters_to_plot	Character vector of clusters to include in the plots
pos_marker	Character vector of gene names for positively gating cells. Cells expressing zero counts will be excluded
neg_marker	Character vector of gene names for negatively gating cells. Cells expressing these genes (>0) will be excluded.
plot_type	The appearance of plots. Can be one of the following: "box", "violin", "bar"
add_jitter	Show transparent jitter points (logical)
add_point	Shot aligned points (instead of jitter)
point_size	Size of the jitter points
point_alpha	Transparency of the jitter points
add_mean	Logical. Set it to TRUE if you would like to show mean per group
mean_color	Color of the mean point
add_median	Logical. Set it to TRUE if you would like to median per group
median_color	Color of the median point
sort_plots	Logical. Set it to TRUE to alphabetically sort graphs based on gene name
colors_to_use	Character vector of colors per sample. Default is rainbow palette.
show_stats	Calculate statistical tests and display on graph
comparisons	A list of pairs of character vectors to show comparisons for. list(c(wt, ko1), c("wt", "ko2")). By default, all pairwise comparisons are calculated and plotted.
stat_method	Which statistical test to use. Select one of "wilcox.text" (default) or "t.test".
p_adj_method	How to adjust for multiple comparisons. Possible values are "holm" (default), "hochberg", "hommel", "bonferroni", "BH", "BY","fdr", "none")
y_expand_low	Expand low y-limit as a multiplicative factor (see mult argument of expand_scale())
y_expand_high	Expand high y-limit as a multiplicative factor (see mult argument of expand_scale())
pval_y_offset	Offset factor for determining y-coordinate of p values shown on the plot. It is a multiplicative factor y_max
save_pdf	Save results as a pdf file in the work directory
append_to_filename	String to append to the pdf filename for organizational purposes
output_plot	Logical. Set it to FALSE if you would like to suppress graphical output. Could be helpful for creating pdf files.
assign_global_plotlist	Logical. Creates a global plot_list object to allow further graphical manipulations
show_progress	Logical. Creates a message output to the console to let you know which gene is being analyzed and plotted
image_columns	Controls the number of figure columns on one output page (default is 4)
image_rows	Controls the number of figure rows on one output page (defaul is 4)
...	other parameters to pass to gg

Value

Graphical outputs showing gene expression per sample or cluster

See Also

[df_extractor()]

Examples

# Run function on exprs_df data frame
gene_grapher(exprs = exprs_df,
x_variable = "sample",
genes_to_plot = c("Ifng", "Gzmb", "Pdcd1"),
clusters_to_plot = "T cells",
pos_marker = NULL,
neg_marker = NULL ,
plot_type = "box",
add_jitter = T,
add_mean = T,
mean_color = "black",
add_median = F ,
sort_plots = T,
colors_to_use = cols,
show_stats = T,
comparisons = list(c("Sample1", "Sample2"),
                  c("Sample1", "Sample3")),
stat_method = "wilcox" ,
p_adj_method = "holm" ,
save_pdf = T,
append_to_filename = "_Tcell_genes" ,
output_plot = T,
assign_global_plotlist = F,
show_progress = F,
image_columns = 4,
image_rows = 4,
pval_y_offset = 4/5,
y_expand_high = 0.2)

atakanekiz/SCseqtools documentation built on April 18, 2023, 12:55 a.m.