gspaMap: Volcano plots of protein 'log2FC' under gene sets

In qzhang503/proteoQ: Processing and Informatic Analysis of Mass Spectrometrirc Data

Volcano plots of protein log2FC under gene sets

Description

gspaMap visualizes the volcano plots of protein subgroups under the same gene sets.

Usage

gspaMap(
  gset_nms = c("go_sets", "c2_msig", "kinsub"),
  scale_log2r = TRUE,
  complete_cases = FALSE,
  impute_na = FALSE,
  df = NULL,
  df2 = NULL,
  filepath = NULL,
  filename = NULL,
  fml_nms = NULL,
  adjP = FALSE,
  topn_labels = 20,
  show_sig = "none",
  gspval_cutoff = 0.05,
  gslogFC_cutoff = log2(1.2),
  topn_gsets = Inf,
  theme = NULL,
  ...
)

Arguments

gset_nms	Character string or vector containing the shorthanded name(s), full file path(s), or both, to gene sets for enrichment analysis. For species among "human", "mouse", "rat", the default of c("go_sets", "c2_msig", "kinsub") will utilize terms from gene ontology (GO), molecular signatures (MSig) and kinase-substrate network (PSP Kinase-Substrate). Custom GO, MSig and other data bases at given species are also supported. See also: prepGO for the preparation of custom GO; prepMSig for the preparation of custom MSig. For other custom data bases, follow the same format of list as GO or MSig.
scale_log2r	Logical; if TRUE, adjusts log2FC to the same scale of standard deviation across all samples. The default is TRUE. At scale_log2r = NA, the raw log2FC without normalization will be used.
complete_cases	Logical; if TRUE, only cases that are complete with no missing values will be used. The default is FALSE.
impute_na	Logical; if TRUE, data with the imputation of missing values will be used. The default is FALSE.
df	The name of a primary data file. By default, it will be determined automatically after matching the types of data and analysis with an id among c("pep_seq", "pep_seq_mod", "prot_acc", "gene"). A primary file contains normalized peptide or protein data and is among c("Peptide.txt", "Peptide_pVal.txt", "Peptide_impNA_pVal.txt", "Protein.txt", "Protein_pVal.txt", "protein_impNA_pVal.txt"). For analyses require the fields of significance p-values, the df will be one of c("Peptide_pVal.txt", "Peptide_impNA_pVal.txt", "Protein_pVal.txt", "protein_impNA_pVal.txt").
df2	Character vector or string; the name(s) of secondary data file(s). An informatic task, i.e. anal_prnTrend(...) against a primary df generates secondary files such as Protein_Trend_Z_nclust6.txt etc. See also prnHist for the description of a primary df; normPSM for the lists of df and df2.
filepath	Use system default.
filename	Use system default for each gene set.
fml_nms	Character string or vector; the formula name(s). By default, the formula(s) will match those used in pepSig or prnSig.
adjP	Logical; if TRUE, use Benjamini-Hochberg pVals in volcano plots. The default is FALSE.
topn_labels	A non-negative integer; the top-n species for labeling in a plot. At topn_labels = 0, no labels of proteins/peptides will be shown. The default is to label the top-20 species with the lowest p-values.
show_sig	Character string indicating the type of significance values to be shown with gspaMap. The default is "none". Additional choices are from c("pVal", "qVal") where pVal or qVal will be shown, respectively, in the facet grid of the plots.
gspval_cutoff	Numeric value or vector for uses with gspaMap. Gene sets with enrichment pVals less significant than the threshold will be excluded from volcano plot visualization. The default significance is 0.05 for all formulas matched to or specified in argument fml_nms. Formula-specific threshold is allowed by supplying a vector of cut-off values.
gslogFC_cutoff	Numeric value or vector for uses with gspaMap. Gene sets with absolute enrichment log2FC less than the threshold will be excluded from volcano plot visualization. The default magnitude is log2(1.2) for all formulas matched to or specified in argument fml_nms. Formula-specific threshold is allowed by supplying a vector of absolute values in log2FC.
topn_gsets	Numeric value or vector; top entries in gene sets ordered by increasing pVal for visualization. The default is to use all available entries. Note that it is users' responsibility to ensure that the custom gene sets contain terms that can be found from the one or multiple preceding analyses of prnGSPA. For simplicity, it is generally applicable to include all of the data bases that have been applied to prnGSPA and in that way no terms will be missed for visualization. See also prnGSPA for examples of custom data bases.
theme	A ggplot2 theme, i.e., theme_bw(), or a custom theme. At the NULL default, a system theme will be applied.
...	filter_: Variable argument statements for the row filtration against data in a primary file linked to df. See also normPSM for the format of filter_ statements and the association between filter_ and df. filter2_: Variable argument statements for the row filtration against data in secondary file(s) linked to df2. See also prnGSPAHM for the format of filter2_, normPSM for the association between filter_ and df. Additional parameters for plotting: xco, the cut-off lines of fold changes at position x; the default is at -1.2 and +1.2. yco, the cut-off line of pVal at position y; the default is 0.05. width, the width of plot; height, the height of plot. nrow, the number of rows in a plot.

See Also

Metadata
load_expts for metadata preparation and a reduced working example in data normalization

Data normalization
normPSM for extended examples in PSM data normalization
PSM2Pep for extended examples in PSM to peptide summarization
mergePep for extended examples in peptide data merging
standPep for extended examples in peptide data normalization
Pep2Prn for extended examples in peptide to protein summarization
standPrn for extended examples in protein data normalization.
purgePSM and purgePep for extended examples in data purging
pepHist and prnHist for extended examples in histogram visualization.
extract_raws and extract_psm_raws for extracting MS file names

Variable arguments of 'filter_...'
contain_str, contain_chars_in, not_contain_str, not_contain_chars_in, start_with_str, end_with_str, start_with_chars_in and ends_with_chars_in for data subsetting by character strings

Missing values
pepImp and prnImp for missing value imputation

Informatics
pepSig and prnSig for significance tests
pepVol and prnVol for volcano plot visualization
prnGSPA for gene set enrichment analysis by protein significance pVals
gspaMap for mapping GSPA to volcano plot visualization
prnGSPAHM for heat map and network visualization of GSPA results
prnGSVA for gene set variance analysis
prnGSEA for data preparation for online GSEA.
pepMDS and prnMDS for MDS visualization
pepPCA and prnPCA for PCA visualization
pepLDA and prnLDA for LDA visualization
pepHM and prnHM for heat map visualization
pepCorr_logFC, prnCorr_logFC, pepCorr_logInt and prnCorr_logInt for correlation plots
anal_prnTrend and plot_prnTrend for trend analysis and visualization
anal_pepNMF, anal_prnNMF, plot_pepNMFCon, plot_prnNMFCon, plot_pepNMFCoef, plot_prnNMFCoef and plot_metaNMF for NMF analysis and visualization

Custom databases
Uni2Entrez for lookups between UniProt accessions and Entrez IDs
Ref2Entrez for lookups among RefSeq accessions, gene names and Entrez IDs
prepGO for gene ontology
prepMSig for molecular signatures
prepString and anal_prnString for STRING-DB

Column keys in PSM, peptide and protein outputs
system.file("extdata", "psm_keys.txt", package = "proteoQ")
system.file("extdata", "peptide_keys.txt", package = "proteoQ")
system.file("extdata", "protein_keys.txt", package = "proteoQ")

Examples

# ===================================
# Volcano plots
# ===================================

## !!!require the brief working example in `?load_expts`

## global option
scale_log2r <- TRUE

## for all peptides or proteins
# all peptides
pepVol()

# all proteins
prnVol(
  xco = 1.2,
  yco = 0.01,
)

# hide `xco` and/or `yco` lines
# (xco = 0 -> log2(xco) = - Inf)
prnVol(
  xco = 0,
  yco = Inf,
  filename = no_xylines.png,
)

# shows vertical center line at log2(1)
# (xco = 1 -> log2(xco) = 0)
prnVol(
  xco = 1,
  yco = Inf,
  filename = no_xylines.png,
)

# kinases and prot_n_pep >= 2
prnVol(
  xco = 1.2,
  yco = 0.01,
  filter_prots_by_kin = exprs(kin_attr, prot_n_pep >= 2),
  filename = "kin_npep2.png"
)

# selected formula and/or customization
prnVol(
  fml_nms = "W2_bat",
  xmin = -5,
  xmax = 5, 
  ymin = 0, 
  ymax = 30,
  x_label = "Ratio ("*log[2]*")",
  y_label = "pVal ("*-log[10]*")", 
  height = 6,
  width = 6*2.7,
  filename = custom.png,
)

# custom theme
library(ggplot2)
my_theme <- theme_bw() +
  theme(
    axis.text.x = element_text(angle = 0, vjust = 0.5, size = 24),
    axis.ticks.x = element_blank(),
    axis.text.y = element_text(angle = 0, vjust = 0.5, size = 24),
    axis.title.x = element_text(colour = "black", size = 24),
    axis.title.y = element_text(colour="black", size = 24),
    plot.title = element_text(face = "bold", colour = "black", size = 14, 
                              hjust = .5, vjust = .5),
    
    panel.grid.major.x = element_blank(),
    panel.grid.minor.x = element_blank(),
    panel.grid.major.y = element_blank(),
    panel.grid.minor.y = element_blank(),
    
    strip.text.x = element_text(size = 16, colour = "black", angle = 0),
    strip.text.y = element_text(size = 16, colour = "black", angle = 90),
    
    legend.key = element_rect(colour = NA, fill = 'transparent'),
    legend.background = element_rect(colour = NA,  fill = "transparent"),
    legend.position = "none",
    legend.title = element_text(colour="black", size = 18),
    legend.text = element_text(colour="black", size = 18),
    legend.text.align = 0,
    legend.box = NULL
  )

prnVol(theme = my_theme, filename = my_theme.png)

# custom plot
# ("W2_bat" etc. are contrast names in `pepSig`)
prnVol(fml_nms = c("W2_bat", "W2_loc"), filename = foo.png)

res <- readRDS(file.path(dat_dir, "Protein/Volcano/W2_bat/foo.rds"))
# names(res)

p <- ggplot() +
  geom_point(data = res$data, mapping = aes(x = log2Ratio, y = -log10(pVal)), 
             size = 3, colour = "#f0f0f0", shape = 20, alpha = .5) +
  geom_point(data = res$greater, mapping = aes(x = log2Ratio, y = -log10(pVal)), 
             size = 3, color = res$palette[2], shape = 20, alpha = .8) +
  geom_point(data = res$less, mapping = aes(x = log2Ratio, y = -log10(pVal)), 
             size = 3, color = res$palette[1], shape = 20, alpha = .8) +
  geom_hline(yintercept = -log10(res$yco), linetype = "longdash", size = .5) +
  geom_vline(xintercept = -log2(res$xco), linetype = "longdash", size = .5) +
  geom_vline(xintercept = log2(res$xco), linetype = "longdash", size = .5) +
  scale_x_continuous(limits = c(res$xmin, res$xmax)) +
  scale_y_continuous(limits = c(res$ymin, res$ymax)) +
  labs(title = res$title, x = res$x_label, y = res$y_label) +
  res$theme

p <- p + geom_text(data = res$topns, 
                   mapping = aes(x = log2Ratio, 
                                 y = -log10(pVal), 
                                 label = Index, 
                                 color = Index),
                   size = 3, 
                   alpha = .5, 
                   hjust = 0, 
                   nudge_x = 0.05, 
                   vjust = 0, 
                   nudge_y = 0.05, 
                   na.rm = TRUE)

p <- p + facet_wrap(~ Contrast, nrow = 1, labeller = label_value)

p <- p + geom_table(data = res$topn_labels, aes(table = gene), 
                    x = -res$xmax*.85, y = res$ymax/2)

# Highlight
prnVol(
  highlights = rlang::exprs(gene %in% c("ACTB", "GAPDH")), 
  filename = highlights.png
)


## protein subgroups by gene sets
# prerequisite analysis of GSPA
prnGSPA(
  impute_na = FALSE,
  pval_cutoff = 1E-2, # protein pVal threshold
  logFC_cutoff = log2(1.1), # protein log2FC threshold
  gspval_cutoff = 5E-2, # gene-set pVal threshold
  gslogFC_cutoff = log2(1.2), # gene-set log2FC threshold
  gset_nms = c("go_sets"),
)

# mapping gene sets to volcano-plot visualization
# (1) forced lines of `pval_cutoff` and `logFC_cutoff`  
#   according to the corresponding `prnGSPA` in red; 
# (2) optional lines of `xco` and `yco` in grey
gspaMap(
  impute_na = FALSE,
  topn_gsets = 20, 
  show_sig = pVal, 
)

# disable the lines of `xco` and `yco`, 
gspaMap(
  impute_na = FALSE,
  topn_gsets = 20, 
  show_sig = pVal, 
  xco = 0, 
  yco = Inf, 
)

# customized thresholds for visualization
gspaMap(
  fml_nms = c("W2_bat", "W2_loc", "W16_vs_W2"),
  gspval_cutoff = c(5E-2, 5E-2, 1E-10),
  gslogFC_cutoff = log2(1.2),
  topn_gsets = 20, 
  topn_labels = 0,
  show_sig = pVal,
  xco = 0, 
  yco = Inf, 
)

## gspaMap(...) maps secondary results of `[...]Protein_GSPA_{NZ}[_impNA].txt` 
#  from prnGSPA(...) onto a primary `df` of `Protein[_impNA]_pVal.txt` 
#  
#  see also ?prnGSPA for additional examples involving both `df` and `df2`, 
#  as well as `filter_` and `filter2_`

qzhang503/proteoQ documentation built on Dec. 14, 2024, 12:27 p.m.