Skip to contents

Create a volcano plot from differential expression data

volcano_plot.Rd

volcano_plot() generates a volcano plot to visualize results from differential expression analysis stored in a data frame. Use this function directly if differential expression results are in a separate data frame and not an spe object Helper function for volcanoPlot_DiffExSpe.R; use volcanoPlot_DiffExSpe.R if differential expression results are in an spe object. -log10(p-value) vs. log2(fold change)

Usage

volcano_plot(
  diffex.spe,
  logFC_colname,
  pval_colname,
  pval_corrected = TRUE,
  log_transformed = TRUE,
  title,
  thresh = 0.05,
  sigLabel_colname
)

Arguments

diffex.spe

A SpatialExperiment object containing differentail expression results in rowData

logFC_colname

column name in differenital expression results that represents log10 fold change

pval_colname

column name in differential epxression results that represents the p-value to be plotted

pval_corrected

Boolean indicating whether pval_colname represents the corrected p-value or not

log_transformed

set to TRUE if data is log transformed

title

title for the plot

thresh

Threshold for p-value to be used to annotate significant results on the plot

sigLabel_colname

Either a a vector with labels or a string (Example: "Gene") that is the column name in differential expression results that should be used for labeling significant results on the plot.

Value

ggplot Volcano plot

Examples

data(smallPancData)
data(pancMeta)
data(protMeta)
pooledData <- dplyr::bind_cols(smallPancData)
pooled.panc.spe <- convert_to_spe(pooledData,
  pancMeta,
  protMeta,
  feature_meta_colname = "pancProts",
  sample_id = ""
)
#> Spatial object created without spatial coordinate 
#>          column names provided. Distance based analysis will not be enabled.
#> Note: Only mapping metadata for 2986 features out of 3000 data points
diffex.spe <- calc_spatial_diff_ex(pooled.panc.spe,
  category_col = "IsletOrNot"
)
#> Warning: Partial NA coefficients for 2 probe(s)
#> We found 0 features with a logFC greater than 1 and 
#>                  an ajusted p-value less than 0.05
volcano_plot(diffex.spe,
  sigLabel_colname = "PrimaryGeneName",
  title = "Islet vs nonIslet"
)
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_point()`).
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_text_repel()`).
#> Warning: ggrepel: 447 unlabeled data points (too many overlaps). Consider increasing max.overlaps