DO Bar plot for GSEA df result

This function generates a split barplot. This is a plot where the top 10 Go terms are shown, sorted based on a column ('col_split'). Two conditions are shown at the same time. One condition is shown in the positive axis, while the other in the negative one. The condition to be shown as positive is set with 'pos_col'.

The GO terms will be shown inside the bars, if the term is too long, using 'cutoff', you can control the maximum number of characters per line.

Pre-filter of the dataframe to contain significant Terms is recommended

Usage

DO.SplitBarGSEA(
  df_GSEA,
  term_col,
  col_split,
  cond_col,
  pos_cond,
  cutoff = 40,
  log10_transform = TRUE,
  figsize = c(12, 8),
  topN = 10,
  colors_pairs = c("sandybrown", "royalblue"),
  alpha_colors = 0.3,
  path = NULL,
  spacing = 5,
  txt_size = 12,
  filename = "SplitBar.svg",
  title = "Top 10 GO Terms in each Condition: ",
  showP = F,
  celltype = "all"
)

Arguments

df_GSEA

dataframe with the results of a gene set enrichment analysis

term_col

column in the dataframe that contains the terms

col_split:

column in the dataframe that will be used to sort and split the plot

cond_col:

column in the dataframe that contains the condition information

pos_cond:

condition that will be shown in the positive side of the plot

cutoff:

maximum number of characters per line

log10_transform:

if col_split contains values between 0 and 1, assume they are pvals and apply a -log10 transformation

figsize:

figure size

topN:

how many terms are shown

path:

path to save the plot

filename:

filename for the plot

spacing:

space to add between bars and origin. It is a percentage value, indicating that the bars start at 5 % of the maximum X axis value.

txt_size:

size of the go terms text

alpha_colors:

alpha value for the colors of the bars

colors_pairs:

colors for each condition (1st color –> negative axis; 2nd color –> positive axis)

title:

title of the plot

showP:

if False, the axis is return

Value

: None or the axis

Author

Mariano Ruz Jurado

Examples

if (FALSE) { # \dontrun{
#df with GSEA results e.g. Metascape results
df_GSEA <- read.csv("path/to/GSEA_results.csv")

#Please add a 'celltype' and 'condition' column
head(df_GSEA)
#Columns should include: "Term", "Combined.Score", "conditon", "celltype", etc.

#Run SplitBarGSEA visualization
DO.SplitBarGSEA(df_GSEA = df_GSEA,
                term_col = "Term",
                col_split = "Combined.Score",
                cond_col = "condition",          # condition column (e.g., experimental group)
                pos_cond = "Treatment",
                cutoff = 40,                 # max term length before truncation
                log10_transform = TRUE,
                figsize = c(12, 8),
                topN = 10,                   # top N GO terms to show
                color_pairs = c("sandybrown", "royalblue"),
                alpha_colors = 0.3,
                path = "results/plots",
                spacing = 5,
                txt_size = 12,
                filename = "SplitBar.svg",
                title = "Top 10 GO Terms in each Condition: ",
                showP = FALSE,
                celltype = "all")
} # }