BIC)

sp_volcano_plot

R Documentation

Generating volcano plot

Description

Generating volcano plot

Usage

sp_volcano_plot(
  data,
  geneL = NULL,
  log2fc_var = "log2FoldChange",
  fdr_var = "padj",
  coordinate_flip = FALSE,
  status_col_var = NULL,
  significance_threshold = c(0.05, 1),
  status_col_var_order = NULL,
  point_color_vector = c("#E6AAAA", "#9AD7EA", "#E6E5E5"),
  log10_transform_fdr = TRUE,
  max_allowed_log10p = Inf,
  max_allowed_log2fc = Inf,
  title = NULL,
  point_label_var = NULL,
  log2fc_symmetry = TRUE,
  alpha = NA,
  point_size = NULL,
  extra_ggplot2_cmd = NULL,
  filename = NULL,
  xtics_angle = 0,
  x_label = "Log2 fold change",
  y_label = "Negative log10 transformed qvalue",
  legend.position = "top",
  xintercept = "fc",
  yintercept = "fdr",
  ...
)

Arguments

`data`	Data frame or data file (with header line, the first column will not be treated as the rowname, tab separated)
`geneL`	Data frame or data file (with header line, the first column will not be treated as the rowname, tab separated)
`log2fc_var`	Name of fold change column.
`fdr_var`	Name of FDR or p-value column.
`coordinate_flip`	Default FALSE meaning `log2fc_var` in `X-axis`. Specify `TRUE` to make `fdr_var` in `X-axis`.
`status_col_var`	Name of the column containing labels of gene expression status like `⁠"No differnece", "UP-regulated", "Down-regulated"⁠`. If exists, this column would be used to color each group of points. This parameter has higher priority than `significance_threshold`.
`significance_threshold`	Set the threshold for defining DE genes in format like `c(pvalue,abs_log_fodchange)`. If this parameter is given, the program will generate `status_col_var` based on given thresholds.
`status_col_var_order`	Changing the order of status column values. Normally, the unique values of status column would be sorted alphabetically. For example, the order of `⁠"No difference", "UP-regulated", "Down-regulated"⁠` would be `⁠"Down-regulated", "No differnece", "UP-regulated"⁠`. Here we can specify their order manually like `⁠"UP-regulated", "Down-regulated", "No differnece"⁠` to match the color specified below.
`point_color_vector`	Color vector. Default 'red, green, grey' for 'up, dw, nodiff' when `status_col_var` is not given. The order of color vector must match the order of levels of `status_col_var`.
`log10_transform_fdr`	Get `-log10(pvalue)` or `-log10(fdr)` for column given to `fdr_var`. Default FALSE, accept TRUE.
`max_allowed_log10p`	Maximum allowed `-log10(pvalue)`. Default `Inf` meaning no limitation. Normally this should be set to 3 or 4 to make the output picture beautiful.
`max_allowed_log2fc`	Maximum allowed `log2(foldchange)`. Default `Inf` meaning no limitation. Normally this should be set to 3 or 4 to make the output picture beautiful.
`title`	Title of picture.
`point_label_var`	Name of columns containing labels for points (representing genes, proteins or OTUs) to be labeled. Points with `NA`,`-` or “ value in this column will not be labeled.
`log2fc_symmetry`	Make coordinate axis symmetry to generate better visualization. Default TRUE.
`alpha`	Transparency of points (0-1). 0: opaque; 1: transparent.
`point_size`	Point size. Default 0.8. Accept a number of name of one column.
`extra_ggplot2_cmd`	Extra ggplot2 commands (currently unsupported)
`filename`	Output picture to given file.
`xtics_angle`	Rotation angle for a-axis. Default 0.
`x_label`	Xlab label.Default "Log2 fold change".
`y_label`	Ylab label.Default "Negative log10 transformed qvalue".
`legend.position`	Position of legend, accept top, bottom, left, right, none or c(0.8,0.8).
`xintercept`	Default 'fc' to show fold change lines. This needs `significance_threshold`. Specify NULL to hide lines.
`yintercept`	Default 'fdr' to show fdr lines. This needs `significance_threshold`. Specify NULL to hide lines.
`...`	Parameters given to `sp_ggplot_layout`

Value

A ggplot2 object

Examples


### Generate test data
res_output <- data.frame(log2FoldChange=rnorm(3000), row.names=paste0("ImageGP",1:3000))
res_output$padj <- 20 ^ (-1*(res_output$log2FoldChange^2))
padj = 0.05
log2FC = 1
res_output$level <- ifelse(res_output$padj<=padj,
                           ifelse(res_output$log2FoldChange>=log2FC,
                                  paste("groupA","UP"),
                                  ifelse(res_output$log2FoldChange<=(-1)*(log2FC),
                                         paste("groupB","UP"), "NoDiff")) , "NoDiff")
head(res_output)

volcanoPlot(res_output, )

## Not run:
input <- "KO-OE_all.txt"
volcano_plot(input,log2fc_var='Log2FoldChange',fdr_var='Padj',status_col_var='',
             title="sd",label="Label",log10_transform_fdr=TRUE,point_size=5)
## End(Not run)

Tong-Chen/ImageGP documentation built on April 14, 2025, 12:54 p.m.