R/createDomainPlot.R
In BIONF/PhyloProfile: PhyloProfile
Defines functions
addFeatureColors
linearizeArchitecture
resolveOverlapFeatures
checkOverlapDomains
joinPlotMergeLegends
modifyFeatureName
sortDomainsByList
sortDomains
pairDomainPlotting
singleDomainPlotting
createArchiPlot
Documented in
addFeatureColors
checkOverlapDomains
createArchiPlot
joinPlotMergeLegends
linearizeArchitecture
modifyFeatureName
pairDomainPlotting
resolveOverlapFeatures
singleDomainPlotting
sortDomains
sortDomainsByList
#' Create protein's domain architecure plot
#' @description Create architecture plot for both seed and orthologous protein.
#' If domains of ortholog are missing, only architecture of seed protein will
#' be plotted. NOTE: seed protein ID is the one being shown in the profile plot,
#' which normally is also the orthologous group ID.
#' @export
#' @usage createArchiPlot(info, domainDf, labelArchiSize, titleArchiSize,
#' showScore, showWeight, namePosition, firstDist, nameType, nameSize,
#' segmentSize, nameColor, labelPos, colorType, ignoreInstanceNo,
#' currentNCBIinfo, featureClassSort, featureClassOrder, colorPalette,
#' resolveOverlap, font)
#' @param info A list contains seed and ortholog's IDs
#' @param domainDf Dataframe contains domain info for the seed and ortholog.
#' This including the seed ID, orthologs IDs, sequence lengths, feature names,
#' start and end positions, feature weights (optional) and the status to
#' determine if that feature is important for comparison the architecture
#' between 2 proteins* (e.g. seed protein vs ortholog) (optional).
#' @param labelArchiSize Lable size (in px). Default = 12.
#' @param titleArchiSize Title size (in px). Default = 12.
#' @param showScore Show/hide E-values and Bit-scores. Default = NULL (hide)
#' @param showWeight Show/hide feature weights. Default = NULL (hide)
#' @param namePosition list of positions for domain names, choose from "plot",
#' "legend" or "axis". Default: "plot"
#' @param firstDist Distance of the first domain to plot title. Default = 0.5
#' @param nameType Type of domain names, either "Texts" or "Labels" (default)
#' @param nameSize Size of domain names. Default = 3
#' @param segmentSize Height of domain segment. Default = 5
#' @param nameColor Color of domain names (for Texts only). Default = "black"
#' @param labelPos Position of domain names (for Labels only). Choose from
#' @param colorType Choose to color "all", "shared", "unique" features or color
#' by "Feature type". Default = "all"
#' @param ignoreInstanceNo Ignore number of feature instances while identifying
#' shared or unique features. Default = FALSE
#' @param currentNCBIinfo Dataframe of the pre-processed NCBI taxonomy
#' data. Default = NULL (will be automatically retrieved from PhyloProfile app)
#' @param featureClassSort Choose to sort features. Default = "Yes"
#' @param featureClassOrder vector of ordered feature classes
#' @param colorPalette Choose between "Paired", "Set1", "Set2", "Set3",
#' "Accent", "Dark2" for the color pallete
#' @param resolveOverlap Choose to merge non-overlapped features of a feature
#' type into one line. Default = "Yes"
#' @param font font of text. Default = Arial"
#' @return A domain plot as arrangeGrob object. Use grid::grid.draw(plot) to
#' render.
#' @author Vinh Tran tran@bio.uni-frankfurt.de
#' @importFrom stringr str_count
#' @seealso \code{\link{singleDomainPlotting}},\code{\link{pairDomainPlotting}},
#' \code{\link{sortDomains}}, \code{\link{parseDomainInput}}
#' @examples
#' seedID <- "101621at6656"
#' orthoID <- "101621at6656|AGRPL@224129@0|224129_0:001955|1"
#' info <- c(seedID, orthoID)
#' domainFile <- system.file(
#' "extdata", "domainFiles/101621at6656.domains",
#' package = "PhyloProfile", mustWork = TRUE
#' )
#' domainDf <- parseDomainInput(seedID, domainFile, "file")
#' domainDf$feature_id_mod <- domainDf$feature_id
#' domainDf$feature_id_mod <- gsub("SINGLE", "LCR", domainDf$feature_id_mod)
#' domainDf$feature_id_mod[domainDf$feature_type == "coils"] <- "Coils"
#' domainDf$feature_id_mod[domainDf$feature_type == "seg"] <- "LCR"
#' domainDf$feature_id_mod[domainDf$feature_type == "tmhmm"] <- "TM"
#' plot <- createArchiPlot(info, domainDf, font = "sans")
#' grid::grid.draw(plot)
createArchiPlot <- function(
info = NULL, domainDf = NULL, labelArchiSize = 12, titleArchiSize = 12,
showScore = NULL, showWeight = NULL, namePosition = "plot",
firstDist = 0.5, nameType = "Labels", nameSize = 3, segmentSize = 5,
nameColor = "#000000", labelPos = "Above", colorType = "Unique",
ignoreInstanceNo = FALSE, currentNCBIinfo = NULL,
featureClassSort = "Yes", featureClassOrder = NULL,
colorPalette = "Paired", resolveOverlap = "Yes", font = "Arial"
){
if (is.null(info) | is.null(domainDf)) return(ggplot() + theme_void())
group <- as.character(info[1])
ortho <- as.character(info[2])
# get sub dataframe based on selected groupID and orthoID
group <- gsub("\\|", ":", group)
ortho <- gsub("\\|", ":", ortho)
grepID <- paste(group, "#", ortho, sep = "")
subdomainDf <- domainDf
subdomainDf$feature <- as.character(subdomainDf$feature)
subdomainDf <- subdomainDf[!duplicated(subdomainDf), ]
orthoID <- NULL
if (nrow(subdomainDf) < 1) return(paste0("No domain info available!"))
else {
# get minStart and maxEnd
minStart <- min(subdomainDf$start)
maxEnd <- max(subdomainDf$end)
if ("length" %in% colnames(subdomainDf))
maxEnd <- max(c(subdomainDf$end, subdomainDf$length))
# ortho & seed domains df
orthoDf <- subdomainDf[subdomainDf$orthoID == ortho,]
seedDf <- subdomainDf[subdomainDf$orthoID != ortho,]
if (nrow(seedDf) == 0) seedDf <- orthoDf
seed <- as.character(seedDf$orthoID[1])
if (nrow(seedDf) == 0) return(paste0("No domain info available!"))
# simplify seed/ortho seq IDs if they are in bionf format
if (!is.null(currentNCBIinfo)) {
if (
stringr::str_count(seed, ":") >= 2 &
stringr::str_count(seed, "@") >= 2
) {
seedTmp <- strsplit(as.character(seed),':', fixed = TRUE)[[1]]
seedSpec <-
strsplit(as.character(seedTmp[2]),'@', fixed = TRUE)[[1]][2]
seed <- paste0(
id2name(seedSpec, currentNCBIinfo)[,2], " - ", seedTmp[3]
)
if (ortho != seed) {
orthoTmp <- strsplit(
as.character(ortho),':', fixed = TRUE)[[1]]
orthoSpec <-
strsplit(
as.character(orthoTmp[2]),'@',fixed = TRUE)[[1]][2]
ortho <- paste0(
id2name(orthoSpec, currentNCBIinfo)[,2],
" - ", orthoTmp[3]
)
}
}
}
# add feature colors
featureColorDf <- addFeatureColors(
seedDf, orthoDf, colorType, colorPalette, ignoreInstanceNo
)
seedDf <- featureColorDf[[1]]
orthoDf <- featureColorDf[[2]]
# resolve (non)overlapped features
if (resolveOverlap == "Yes") {
seedDf <- resolveOverlapFeatures(seedDf)
orthoDf <- resolveOverlapFeatures(orthoDf)
} else {
seedDf$featureOri <- seedDf$feature
seedDf$featureOri <- as.character(seedDf$featureOri)
orthoDf$featureOri <- orthoDf$feature
orthoDf$featureOri <- as.character(orthoDf$featureOri)
}
if (nrow(orthoDf) > 0) {
if (all.equal(seedDf, orthoDf)[1] == TRUE) featureClassSort <- "No"
# sort features
if (featureClassSort == "Yes") {
# change order of one df's features based on order of other df's
if (length(orthoDf$feature) < length(seedDf$feature)) {
orderedOrthoDf <- orthoDf[order(orthoDf$feature), ]
orderedSeedDf <- sortDomains(orderedOrthoDf, seedDf)
orderedOrthoDf <- sortDomains(orderedSeedDf, orderedOrthoDf)
} else {
orderedSeedDf <- seedDf[order(seedDf$feature), ]
orderedOrthoDf <- sortDomains(orderedSeedDf, orthoDf)
orderedSeedDf <- sortDomains(orderedOrthoDf, orderedSeedDf)
}
} else {
# change order based on list of feature types
orderedSeedDf <- sortDomainsByList(seedDf, featureClassOrder)
orderedOrthoDf <- sortDomainsByList(orthoDf, featureClassOrder)
}
# plotting
g <- pairDomainPlotting(
seed, ortho, orderedSeedDf, orderedOrthoDf, minStart, maxEnd,
labelArchiSize, titleArchiSize, showScore, showWeight,
namePosition, firstDist, nameType, nameSize, segmentSize,
nameColor, labelPos, colorPalette, font)
} else {
orderedSeedDf <- sortDomainsByList(seedDf, featureClassOrder)
# plotting
g <- pairDomainPlotting(
seed, seed, orderedSeedDf, orderedSeedDf, minStart, maxEnd,
labelArchiSize, titleArchiSize, showScore, showWeight,
namePosition, firstDist, nameType, nameSize, segmentSize,
nameColor, labelPos, colorPalette, font)
}
return(g)
}
}
#' Create architecure plot for a single protein
#' @usage singleDomainPlotting(df, geneID, sep, labelSize, titleSize, minStart,
#' maxEnd, colorPalette, showScore, showWeight, namePosition, firstDist,
#' nameType, nameSize, segmentSize, nameColor, labelPos, font)
#' @param df Domain dataframe for ploting containing the seed ID, ortholog ID,
#' ortholog sequence length, feature names, start and end positions,
#' feature weights (optional) and the status to determine if that feature is
#' important for comparison the architecture between 2 proteins* (e.g. seed
#' protein vs ortholog) (optional)
#' @param geneID ID of seed or orthologous protein
#' @param sep Separate indicator for title. Default = "|"
#' @param labelSize Lable size. Default = 12
#' @param titleSize Title size. Default = 12
#' @param minStart The smallest start position of all domains
#' @param maxEnd The highest stop position of all domains
#' @param colorPalette Color pallete. Default = Paired"
#' @param showScore Show/hide E-values and Bit-scores. Default = NULL (hide)
#' @param showWeight Show/hide feature weights. Default = NULL (hide)
#' @param namePosition List of positions for domain names, choose from "plot",
#' "legend" or "axis". Default: "plot"
#' @param firstDist Distance of the first domain to plot title. Default = 0.5
#' @param nameType Type of domain names, either "Texts" or "Labels" (default)
#' @param nameSize Size of domain names. Default = 3
#' @param segmentSize Height of domain segment. Default = 5
#' @param nameColor Color of domain names (for Texts only). Default = "black"
#' @param labelPos Position of domain names (for Labels only). Choose from
#' "Above" (default), "Below" or "Inside" the domain bar
#' @param font font of text. Default = Arial"
#' @return Domain plot of a single protein as a ggplot object.
#' @author Vinh Tran tran@bio.uni-frankfurt.de
#' @importFrom RColorBrewer brewer.pal
#' @importFrom stringr str_wrap
#' @seealso \code{\link{parseDomainInput}}
#' @import ggplot2
#' @examples
#' seed <- "101621at6656"
#' ortho <- "101621at6656|AGRPL@224129@0|224129_0:001955|1"
#' ortho <- gsub("\\|", ":", ortho)
#' grepID <- paste(seed, "#", ortho, sep = "")
#' domainFile <- system.file(
#' "extdata", "domainFiles/101621at6656.domains",
#' package = "PhyloProfile", mustWork = TRUE
#' )
#' domainDf <- parseDomainInput(seed, domainFile, "file")
#' domainDf$feature_id_mod <- domainDf$feature_id
#' subdomainDf <- domainDf[grep(grepID, domainDf$seedID), ]
#' subdomainDf$feature <- as.character(subdomainDf$feature)
#' orthoDf <- subdomainDf[subdomainDf$orthoID == ortho,]
#' seedDf <- subdomainDf[subdomainDf$orthoID != ortho,]
#' minStart <- min(subdomainDf$start)
#' maxEnd <- max(c(subdomainDf$end, subdomainDf$length))
#' # resolve overlapping domains
#' seedDf <- PhyloProfile:::resolveOverlapFeatures(seedDf)
#' orthoDf <- PhyloProfile:::resolveOverlapFeatures(orthoDf)
#' # add feature colors
#' featureColorDf <- PhyloProfile:::addFeatureColors(seedDf, orthoDf)
#' seedDf <- featureColorDf[[1]]
#' orthoDf <- featureColorDf[[2]]
#' # do plot
#' g <- PhyloProfile:::singleDomainPlotting(
#' seedDf, seed, minStart = minStart, maxEnd = maxEnd, font = "sans"
#' )
#' grid::grid.draw(g)
singleDomainPlotting <- function(
df = NULL, geneID = "GeneID", sep = "|", labelSize = 12, titleSize = 12,
minStart = NULL, maxEnd = NULL, colorPalette = "Set2",
showScore = NULL, showWeight = NULL, namePosition = "plot",
firstDist = 0.5, nameType = "Labels", nameSize = 3, segmentSize = 5,
nameColor = "#000000", labelPos = "Above", font = "Arial"
){
feature <- feature_id_mod <- end <- start <- featureOri <- NULL
evalue <- bitscore <- weight <- NULL
# parse parameters
if (is.null(df)) return(ggplot() + theme_void())
if (is.null(minStart)) minStart <- min(df$start)
if (is.null(maxEnd)) maxEnd <- max(df$end)
if ("color" %in% colnames(df)) {
colorScheme <- structure(
df$color, .Names = df$featureOri
)
} else {
colorScheme <- structure(
head(
suppressWarnings(
RColorBrewer::brewer.pal(
nlevels(as.factor(df$feature)), colorPalette
)
),
levels(as.factor(df$feature))
),
.Names = levels(as.factor(df$feature)))
}
# initiate ggplot object
gg <- ggplot(df, aes(y = feature, x = end))
# draw lines for representing sequence length
if ("length" %in% colnames(df)) {
gg <- gg + geom_segment(
data = df, linewidth = 0.6, color = "#b2b2b2", alpha = 0.5,
aes(x = 0, xend = length, y = feature, yend = feature))
}
# draw features
gg <- gg + geom_segment(
data = df, aes(
x = start, xend = end, y = feature, yend = feature,
color = as.factor(featureOri)
), linewidth = segmentSize, alpha = 1.0) +
scale_color_manual(values = colorScheme)
# add feature names
if ("plot" %in% namePosition) {
if (nameType == "Labels") {
if (labelPos == "Above") {
gg <- gg + geom_label(
aes(
label = stringr::str_wrap(feature_id_mod),
x = (start+end)/2
),
color = "black", vjust = -0.5, size = nameSize, family=font
)
} else if (labelPos == "Below") {
gg <- gg + geom_label(
aes(
label = stringr::str_wrap(feature_id_mod),
x = (start+end)/2
),
color = "black", vjust = 1.5, size = nameSize, family = font
)
} else {
gg <- gg + geom_label(
aes(
label = stringr::str_wrap(feature_id_mod),
x = (start+end)/2
),
color = "black", size = nameSize, family = font
)
}
} else {
gg <- gg + geom_text(
aes(
label = stringr::str_wrap(feature_id_mod),
x = (start+end)/2
),
color = nameColor, check_overlap = TRUE, size = nameSize,
family = font
)
}
}
# add scores if selected
if ("Bit-score" %in% showScore & "E-value" %in% showScore) {
gg <- gg + geom_label(
aes(
label = ifelse(
evalue == "NA" & bitscore == "NA", "", stringr::str_wrap(
paste0("E-value: ", evalue, "; Bitscore: ", bitscore)
)
), x = (start+end)/2
), color = "black", vjust = 1.25
)
} else if ("Bit-score" %in% showScore) {
gg <- gg + geom_label(
aes(
label = ifelse(bitscore == "NA", "", stringr::str_wrap(
paste0("Bitscore: ", bitscore)
)), x = (start+end)/2
), color = "black", vjust = 1.25
)
} else if ("E-value" %in% showScore) {
gg <- gg + geom_label(
aes(
label = ifelse(evalue == "NA", "", stringr::str_wrap(
paste0("E-value: ", evalue)
)), x = (start+end)/2
), color = "black", vjust = 1.25
)
}
# add weight if selected
if ("Weight" %in% showWeight) {
vjustValue <- 1.25
if ("E-value" %in% showScore | "Bit-score" %in% showScore)
vjustValue <- 2.25
gg <- gg + geom_label(
aes(
label = ifelse(weight == "NA", "", stringr::str_wrap(
paste0("Weight: ", weight)
)), x = (start+end)/2
), color = "black", vjust = vjustValue
)
}
# theme format
gg <- gg + labs(
title = paste0(gsub(":", sep, geneID)), color = "Feature"
)
gg <- gg + theme(
axis.line = element_blank(), axis.ticks.y = element_blank(),
panel.grid.minor.x=element_blank(), panel.grid.major.x=element_blank(),
panel.background = element_blank()
)
gg <- gg + theme(
plot.title = element_text(face = "bold", size = titleSize, hjust = 0.5)
)
gg <- gg + theme(
axis.title = element_blank(),
axis.text.x = element_text(size = labelSize))
gg <- gg + theme(text = element_text(family = font))
# add feature names on the axis (if required)
if ("axis" %in% namePosition) {
if ("plot" %in% namePosition | "legend" %in% namePosition) {
gg <- gg + scale_y_discrete(
expand = c(0.075, 0), breaks = df$feature,
labels = df$feature_type)
} else {
gg <- gg + scale_y_discrete(
expand = c(0.075, 0), breaks = df$feature, labels = df$feature)
}
gg <- gg + theme(axis.text.y = element_text(size = labelSize))
} else {
gg <- gg + theme(axis.text.y = element_blank())
}
# add legend (if required)
if ("legend" %in% namePosition) {
gg <- gg + theme(legend.position = "bottom")
} else {
gg <- gg + theme(legend.position = "none")
}
# add space on the top of the plot (for feature name)
gg <- gg + coord_cartesian(
clip = 'off', ylim = c(1, nlevels(as.factor(df$feature)) + firstDist)
)
# scale x-axis to the length of the longest protein
gg <- gg + xlim(0, maxEnd)
return(gg)
}
#' Create architecure plot for a pair of seed and ortholog protein
#' @usage pairDomainPlotting(seed, ortho, seedDf, orthoDf, minStart, maxEnd,
#' labelSize, titleSize, showScore, showWeight, namePosition, firstDist,
#' nameType, nameSize, segmentSize, nameColor, labelPos, colorPalette, font)
#' @param seed Seed ID
#' @param ortho Ortho ID
#' @param seedDf domain dataframe for seed domains containing the seed ID,
#' ortholog ID, sequence length, feature names, start and end positions,
#' feature weights (optional) and the status to determine if that feature is
#' important for comparison the architecture between 2 proteins* (e.g. seed
#' protein vs ortholog) (optional)
#' @param orthoDf domain dataframe for ortholog domains (same format as seedDf)
#' @param minStart the smallest start position of all domains
#' @param maxEnd the highest stop position of all domains
#' @param labelSize lable size. Default = 12
#' @param titleSize title size. Default = 12
#' @param showScore show/hide E-values and Bit-scores. Default = NULL (hide)
#' @param showWeight Show/hide feature weights. Default = NULL (hide)
#' @param namePosition list of positions for domain names, choose from "plot",
#' "legend" or "axis". Default: "plot"
#' @param firstDist distance of the first domain to plot title. Default = 0.5
#' @param nameType type of domain names, either "Texts" or "Labels" (default)
#' @param nameSize Size of domain names. Default = 3
#' @param segmentSize Height of domain segment. Default = 5
#' @param nameColor color of domain names (for Texts only). Default = "black"
#' @param labelPos position of domain names (for Labels only). Choose from
#' "Above" (default), "Below" or "Inside" the domain bar
#' @param colorPalette color pallete. Default = Paired"
#' @param font font of text. Default = Arial"
#' @return Domain plot of a pair proteins as a arrangeGrob object.
#' @author Vinh Tran tran@bio.uni-frankfurt.de
#' @importFrom gridExtra grid.arrange
#' @seealso \code{\link{singleDomainPlotting}}, \code{\link{sortDomains}},
#' \code{\link{parseDomainInput}}
#' @examples
#' seed <- "101621at6656"
#' ortho <- "101621at6656|AGRPL@224129@0|224129_0:001955|1"
#' ortho <- gsub("\\|", ":", ortho)
#' grepID <- paste(seed, "#", ortho, sep = "")
#' domainFile <- system.file(
#' "extdata", "domainFiles/101621at6656.domains",
#' package = "PhyloProfile", mustWork = TRUE
#' )
#' domainDf <- parseDomainInput(seed, domainFile, "file")
#' domainDf$feature_id_mod <- domainDf$feature_id
#' subdomainDf <- domainDf[grep(grepID, domainDf$seedID), ]
#' subdomainDf$feature <- as.character(subdomainDf$feature)
#' orthoDf <- subdomainDf[subdomainDf$orthoID == ortho,]
#' seedDf <- subdomainDf[subdomainDf$orthoID != ortho,]
#' minStart <- min(subdomainDf$start)
#' maxEnd <- max(c(subdomainDf$end, subdomainDf$length))
#' # resolve overlapping domains
#' seedDf <- PhyloProfile:::resolveOverlapFeatures(seedDf)
#' orthoDf <- PhyloProfile:::resolveOverlapFeatures(orthoDf)
#' # add feature colors
#' featureColorDf <- PhyloProfile:::addFeatureColors(seedDf, orthoDf)
#' seedDf <- featureColorDf[[1]]
#' orthoDf <- featureColorDf[[2]]
#' # do plot
#' g <- PhyloProfile:::pairDomainPlotting(
#' seed,ortho,seedDf,orthoDf,minStart,maxEnd, font = "sans"
#' )
#' grid::grid.draw(g)
pairDomainPlotting <- function(
seed = NULL, ortho = NULL, seedDf = NULL, orthoDf = NULL,
minStart = 0, maxEnd = 999, labelSize = 12, titleSize = 12,
showScore = NULL, showWeight = NULL, namePosition = "plot",
firstDist = 0.5, nameType = "Labels", nameSize = 3, segmentSize = 5,
nameColor = "#000000", labelPos = "Above", colorPalette = "Paired",
font = "Arial"
) {
if(is.null(seed) | is.null(ortho) | is.null(seedDf) | is.null(orthoDf))
stop("Seed/Ortho ID or domain dataframe is NULL!")
sep <- "|"
plotSeed <- singleDomainPlotting(
seedDf, seed, sep, labelSize, titleSize, minStart, maxEnd, colorPalette,
showScore, showWeight, namePosition, firstDist, nameType, nameSize,
segmentSize, nameColor, labelPos, font
)
if (ortho == seed) {
g <- plotSeed
} else {
plotOrtho <- singleDomainPlotting(
orthoDf, ortho, sep, labelSize, titleSize, minStart, maxEnd,
colorPalette, showScore, showWeight, namePosition, firstDist,
nameType, nameSize, segmentSize, nameColor, labelPos, font
)
if ("legend" %in% namePosition) {
g <- joinPlotMergeLegends(
seedDf, orthoDf, plotSeed, plotOrtho, position = "bottom", font
)
} else {
seedHeight <- length(levels(as.factor(seedDf$feature)))
orthoHeight <- length(levels(as.factor(orthoDf$feature)))
g <- gridExtra::grid.arrange(
plotSeed, plotOrtho, nrow = 2,
heights = c(seedHeight, orthoHeight)
)
}
}
return(g)
}
#' Sort one domain dataframe based on the other domain dataframe
#' @description Sort domain dataframe of one protein (either seed or ortholog)
#' based on the dataframe of the its paired protein, in order to bring the
#' common domain feature in the same order which make it easy for comparing.
#' @param seedDf data of seed protein
#' @param orthoDf data of ortholog protein
#' @return Dataframe contains sorted domain list.
#' @author Vinh Tran tran@bio.uni-frankfurt.de
#' @examples
#' # get domain data
#' seedID <- "101621at6656"
#' domainFile <- system.file(
#' "extdata", "domainFiles/101621at6656.domains",
#' package = "PhyloProfile", mustWork = TRUE
#' )
#' domainDf <- parseDomainInput(seedID, domainFile, "file")
#' # get seedDf and orthoDf
#' subDf <- domainDf[
#' domainDf$seedID ==
#' "101621at6656#101621at6656:AGRPL@224129@0:224129_0:001955:1",]
#' orthoDf <- subDf[subDf$orthoID == "101621at6656:DROME@7227@1:Q9VG04",]
#' seedDf <- subDf[subDf$orthoID != "101621at6656:DROME@7227@1:Q9VG04",]
#' # sort
#' PhyloProfile:::sortDomains(seedDf, orthoDf)
sortDomains <- function(seedDf, orthoDf){
if (is.null(seedDf) | is.null(orthoDf))
stop("Domain data for seed & ortholog cannot be NULL!")
orderNo <- NULL
# get list of features in seedDf
featureList <- as.data.frame(levels(as.factor(seedDf$feature)))
colnames(featureList) <- c("feature")
# and add order number to each feature
featureList$orderNo <- seq(length(featureList$feature))
# merge those info to orthoDf
orderedOrthoDf <- merge(orthoDf, featureList, all.x = TRUE)
# sort orthoDf
index <- with(orderedOrthoDf, order(orderNo))
orderedOrthoDf <- orderedOrthoDf[index, ]
# convert feature column into a character vector
orderedOrthoDf$feature <- as.character(orderedOrthoDf$feature)
# then convert it back into an ordered factor
# (to keep this order when plotting)
orderedOrthoDf$feature <- factor(
orderedOrthoDf$feature, levels = unique(orderedOrthoDf$feature)
)
# return sorted df
return(orderedOrthoDf)
}
#' Sort one domain dataframe based on list of ordered feature types
#' @description Sort domain dataframe of one protein based on a given list of
#' ordered feature types
#' @param domainDf domain dataframe
#' @param featureClassOrder vector of ordered feature classes
#' @return Dataframe contains sorted domain list.
#' @author Vinh Tran tran@bio.uni-frankfurt.de
#' @importFrom dplyr left_join
#' @examples
#' # get domain data
#' seedID <- "101621at6656"
#' domainFile <- system.file(
#' "extdata", "domainFiles/101621at6656.domains",
#' package = "PhyloProfile", mustWork = TRUE
#' )
#' domainDf <- parseDomainInput(seedID, domainFile, "file")
#' # get seedDf and orthoDf
#' subDf <- domainDf[
#' domainDf$seedID ==
#' "101621at6656#101621at6656:AGRPL@224129@0:224129_0:001955:1",]
#' orthoDf <- subDf[subDf$orthoID == "101621at6656:DROME@7227@1:Q9VG04",]
#' featureClassOrder <- c("pfam", "smart", "tmhmm", "coils", "signalp", "seg",
#' "flps")
#' # sort
#' PhyloProfile:::sortDomainsByList(orthoDf, featureClassOrder)
sortDomainsByList <- function(domainDf = NULL, featureClassOrder = NULL) {
if (is.null(domainDf) | is.null(featureClassOrder))
stop("Domain data or feature type order is NULL!")
featureClassOrder <- rev(featureClassOrder[
featureClassOrder %in% levels(as.factor(domainDf$feature_type))
])
orderedDomainDf <- dplyr::left_join(
data.frame(feature_type = featureClassOrder),
domainDf, by = "feature_type"
)
orderedDomainDf$feature <- factor(
orderedDomainDf$feature, levels = unique(orderedDomainDf$feature)
)
return(orderedDomainDf)
}
#' Modify feature names
#' @description Simplify feature names (e.g. TM for transmembrane domain,
#' LCR for low complexity regions, remove tool names from domain name) and add
#' weight to feature names (if available)
#' @param domainDf domain data as a dataframe object
#' @return Dataframe contains simlified domain names in yLabel column
#' @author Vinh Tran tran@bio.uni-frankfurt.de
#' @examples
#' domainFile <- system.file(
#' "extdata", "domainFiles/101621at6656.domains",
#' package = "PhyloProfile", mustWork = TRUE
#' )
#' seedID <- "101621at6656"
#' domainDf <- parseDomainInput(seedID, domainFile, "file")
#' PhyloProfile:::modifyFeatureName(domainDf)
modifyFeatureName <- function(domainDf = NULL) {
if (is.null(domainDf)) stop("Domain data cannot be NULL!")
domainDf$yLabel <- domainDf$feature_id
domainDf$yLabel[domainDf$yLabel == "transmembrane"] <- "TM"
domainDf$yLabel[domainDf$yLabel == "low complexity regions"] <- "LCR"
domainDf$yLabel[domainDf$yLabel == "low_complexity_regions"] <- "LCR"
return(domainDf)
}
#' Join multiple plots and merge legends
#' @param df1 Data frame for plot 1
#' @param df2 Data frame for plot 2
#' @param plot1 ggplot object of plot 1
#' @param plot2 ggplot object of plot 2
#' @param position position of legend (bottom or right)
#' @param font font of text
#' @return joined plots with merged legend as a grid object
#' @author Vinh Tran tran@bio.uni-frankfurt.de
#' @importFrom gridExtra grid.arrange
#' @examples
#' seed <- "101621at6656"
#' ortho <- "101621at6656|AGRPL@224129@0|224129_0:001955|1"
#' ortho <- gsub("\\|", ":", ortho)
#' grepID <- paste(seed, "#", ortho, sep = "")
#' domainFile <- system.file(
#' "extdata", "domainFiles/101621at6656.domains",
#' package = "PhyloProfile", mustWork = TRUE
#' )
#' domainDf <- parseDomainInput(seed, domainFile, "file")
#' domainDf$feature_id_mod <- domainDf$feature_id
#' subdomainDf <- domainDf[grep(grepID, domainDf$seedID), ]
#' subdomainDf$feature <- as.character(subdomainDf$feature)
#' orthoDf <- subdomainDf[subdomainDf$orthoID == ortho,]
#' seedDf <- subdomainDf[subdomainDf$orthoID != ortho,]
#' minStart <- min(subdomainDf$start)
#' maxEnd <- max(c(subdomainDf$end, subdomainDf$length))
#' # resolve overlapping domains
#' seedDf <- PhyloProfile:::resolveOverlapFeatures(seedDf)
#' orthoDf <- PhyloProfile:::resolveOverlapFeatures(orthoDf)
#' # add feature colors
#' featureColorDf <- PhyloProfile:::addFeatureColors(seedDf, orthoDf)
#' seedDf <- featureColorDf[[1]]
#' orthoDf <- featureColorDf[[2]]
#' # generate plots
#' plotSeed <- PhyloProfile:::singleDomainPlotting(
#' seedDf, seed, minStart = minStart, maxEnd = maxEnd, font = "sans"
#' )
#' plotOrtho <- PhyloProfile:::singleDomainPlotting(
#' orthoDf, ortho, minStart = minStart, maxEnd = maxEnd, font = "sans"
#' )
#' # merge plots
#' PhyloProfile:::joinPlotMergeLegends(
#' seedDf, orthoDf, plotSeed, plotOrtho, "bottom", font = "sans")
joinPlotMergeLegends <- function(
df1 = NULL, df2 = NULL, plot1 = NULL, plot2 = NULL,
position = c("bottom", "right"), font = "Arial")
{
if (is.null(plot1) | is.null(df1)) stop("No plot data given!")
if (is.null(plot2) | is.null(df2))
return(plot1 + theme(legend.position = position))
featureOri <- NULL
# remove legend of the original plots
plot1 <- plot1 + theme(legend.position = "none")
plot2 <- plot2 + theme(legend.position = "none")
# combine plot1 and 2
combined_plot <- gridExtra::grid.arrange(
plot1, plot2, ncol = 1,
heights = c(
length(levels(as.factor(df1$feature))),
length(levels(as.factor(df2$feature)))
)
)
# create a temp plot that contains all features
mergedDf <- rbind(df1, df2)
colorScheme <- structure(
mergedDf$color, .Names = mergedDf$featureOri
)
tmpPlot <- ggplot() +
geom_segment(
data = mergedDf,
aes(
x = 0, xend = 1, y = 1, yend = 1,
color = featureOri
),
linewidth = 5, lineend = "round", alpha = 0.7
) +
scale_color_manual(values = colorScheme) +
labs(color = "Feature") +
theme_minimal() +
theme(legend.position = position, text = element_text(family = font))
# extract legend from the temp plot above
getOnlyLegend <- function(plot) {
plotTable <- ggplot_gtable(ggplot_build(plot))
legendPlot <- which(
vapply(
plotTable$grobs, function(x) x$name, character(1)
) == "guide-box"
)
legend <- plotTable$grobs[[legendPlot]]
return(legend)
}
legend <- getOnlyLegend(tmpPlot)
# final combined plot with shared legend
combined <- gridExtra::grid.arrange(
combined_plot, legend, nrow = 2, heights = c(10, 1)
)
return(combined)
}
#' Identify feature type(s) containing overlapped domains/features
#' @param domainDf input domain dataframe
#' @return List of feature types that have overlapped domains
#' @author Vinh Tran tran@bio.uni-frankfurt.de
#' @importFrom dplyr group_by add_count
#' @examples
#' # get domain data
#' seedID <- "101621at6656"
#' domainFile <- system.file(
#' "extdata", "domainFiles/101621at6656.domains",
#' package = "PhyloProfile", mustWork = TRUE
#' )
#' domainDf <- parseDomainInput(seedID, domainFile, "file")
#' # get seedDf and orthoDf
#' subDf <- domainDf[
#' domainDf$seedID ==
#' "101621at6656#101621at6656:AGRPL@224129@0:224129_0:001955:1",]
#' orthoDf <- subDf[subDf$orthoID == "101621at6656:DROME@7227@1:Q9VG04",]
#' # check overlap features
#' PhyloProfile:::checkOverlapDomains(orthoDf)
checkOverlapDomains <- function(domainDf) {
if (is.null(domainDf)) stop("Domain data cannot be NULL!")
feature_type <- NULL
df <- domainDf[, c("feature", "feature_type", "start", "end")]
df <- data.frame(
df %>% dplyr::group_by(feature_type) %>% dplyr::add_count(feature_type)
)
df$tmp <- paste(df$feature_type, df$end, sep = "_")
overlappedType <- lapply(
df$tmp[df$n > 1],
function (x) {
if (length(df$feature[df$tmp == x]) > 1)
return(df$feature_type[df$tmp == x])
ed <- df$end[df$tmp == x][1]
st <- df$start[df$tmp == x][1]
type <- df$feature_type[df$tmp == x][1]
subDf <- df[
!(df$tmp == x) & df$feature_type == type &
df$start < ed & df$end > st,
]
if (nrow(subDf) > 0) {
if(!(subDf$feature[1] == df$feature[df$tmp == x]))
return(subDf$feature_type)
}
}
)
return(unique(unlist(overlappedType)))
}
#' Modify domain dataframe to resolve overlapped domains/features
#' @param domainDf input domain dataframe
#' @return Domain dataframe with modified feature names that join multiple
#' domains of the same type that are not overlapped
#' @author Vinh Tran tran@bio.uni-frankfurt.de
#' @examples
#' # get domain data
#' seedID <- "101621at6656"
#' domainFile <- system.file(
#' "extdata", "domainFiles/101621at6656.domains",
#' package = "PhyloProfile", mustWork = TRUE
#' )
#' domainDf <- parseDomainInput(seedID, domainFile, "file")
#' # get seedDf and orthoDf
#' subDf <- domainDf[
#' domainDf$seedID ==
#' "101621at6656#101621at6656:AGRPL@224129@0:224129_0:001955:1",]
#' orthoDf <- subDf[subDf$orthoID == "101621at6656:DROME@7227@1:Q9VG04",]
#' # resolve overlapped featuers
#' PhyloProfile:::resolveOverlapFeatures(orthoDf)
resolveOverlapFeatures <- function(domainDf) {
if (is.null(domainDf)) stop("Domain data cannot be NULL!")
overlappedType <- checkOverlapDomains(domainDf)
domainDf$featureOri <- domainDf$feature
domainDf$featureOri <- as.character(domainDf$featureOri)
if (length(overlappedType) > 0) {
domainDf$feature <- ifelse(
!(domainDf$feature_type %in% overlappedType),
domainDf$feature_type,
domainDf$feature
)
} else {
domainDf$feature <- domainDf$feature_type
}
return(domainDf)
}
#' Linearize PFAM/SMART annotations by best e-value/bitscore
#' @export
#' @param domainDf input domain dataframe
#' @param orthoID ID of protein that needs to be linearized
#' @param value type of values that will be used for linearized, either evalue
#' (default) or bitscore
#' @return Domain dataframe of the selected protein after linearization
#' @author Vinh Tran tran@bio.uni-frankfurt.de
#' @importFrom dplyr arrange
#' @examples
#' demoDomainDf <- data.frame(
#' orthoID = rep("protID", 4),
#' start = c(1, 5, 100, 80),
#' end = c(30, 40, 130, 110),
#' evalue = c(0.001, 0.0005, 0.2, 0.004),
#' feature_type = c(rep("pfam", 2), rep("smart", 2)),
#' feature_id = c("pf1", "pf2", "sm1", "sm2")
#' )
#' linearizeArchitecture(demoDomainDf, "protID", "evalue")
linearizeArchitecture <- function(
domainDf = NULL, orthoID = NULL, value = "evalue"
) {
if (is.null(domainDf) | is.null(orthoID)) stop("Input data is NULL!")
evalue <- bitscore <- start <- end <- NULL
# Sort the dataframe by start position and then by evalue or bitscore
if (value == "evalue") {
domainDf <- domainDf %>% dplyr::arrange(start, evalue)
} else if (value == "bitscore") {
domainDf <- domainDf %>% dplyr::arrange(start, bitscore)
} else stop("Incorrect value specified! Either 'evalue' or 'bitscore'")
# Get lines that need to be excluded
pfamRows <- rownames(domainDf[domainDf$orthoID == orthoID &
domainDf$feature_type %in% c("pfam","smart"),])
exclude_lines <- vapply(
seq_len(length(pfamRows)-1),
function(i) {
if (domainDf[pfamRows[i],]$end >= domainDf[pfamRows[i+1],]$start) {
# Exclude the row with the higher evalue / lower bitscore
if (value == "evalue") {
if (
domainDf[pfamRows[i],]$evalue >
domainDf[pfamRows[i+1],]$evalue
) {
return((pfamRows[i]))
} else {
return((pfamRows[i+1]))
}
} else {
if (
domainDf[pfamRows[i],]$bitscore <
domainDf[pfamRows[i+1],]$bitscore
) {
return((pfamRows[i]))
} else {
return((pfamRows[i+1]))
}
}
} else {
return("0")
}
},
character(1)
)
# return domainDf after removing overlapped features with higher e-values
outDf <- domainDf[!(row.names(domainDf) %in% exclude_lines), ]
return(outDf[outDf$orthoID == orthoID,])
}
#' Add colors for each feature/domain
#' @description Add colors to features/domains of 2 domain dataframes. Users can
#' choose to color only the shared features, unique features, all features
#' (default) or based on feature types. Default color pallete is "Paired", but
#' it can be changed.
#' @param seedDf Domain dataframe of seed protein (protein 1)
#' @param orthoDf Domain dataframe of orthologs protein (protein 2)
#' @param colorType Choose to color "all", "shared", "unique" features or color
#' by "Feature type". Default: "all"
#' @param colorPalette Choose between "Paired", "Set1", "Set2", "Set3",
#' "Accent", "Dark2" for the color pallete
#' @param ignoreInstanceNo Ignore number of feature instances while identifying
#' shared or unique features. Default: FALSE
#' @return 2 dataframes (seedDf and orthoDf) with an additional column for the
#' assigned color to each feature instance
#' @author Vinh Tran tran@bio.uni-frankfurt.de
#' @importFrom RColorBrewer brewer.pal
#' @importFrom utils head
#' @importFrom dplyr count
#' @examples
#' # get domain data
#' seedID <- "101621at6656"
#' domainFile <- system.file(
#' "extdata", "domainFiles/101621at6656.domains",
#' package = "PhyloProfile", mustWork = TRUE
#' )
#' domainDf <- parseDomainInput(seedID, domainFile, "file")
#' # get seedDf and orthoDf
#' subDf <- domainDf[
#' domainDf$seedID ==
#' "101621at6656#101621at6656:AGRPL@224129@0:224129_0:001955:1",]
#' orthoDf <- subDf[subDf$orthoID == "101621at6656:DROME@7227@1:Q9VG04",]
#' seedDf <- subDf[subDf$orthoID != "101621at6656:DROME@7227@1:Q9VG04",]
#' # add colors to features
#' PhyloProfile:::addFeatureColors(seedDf, orthoDf)
addFeatureColors <- function(
seedDf = NULL, orthoDf = NULL, colorType = "all",
colorPalette = "Paired", ignoreInstanceNo = FALSE
) {
if (is.null(seedDf) | is.null(orthoDf)) stop("Domain Df cannot be null!")
feature <- NULL
featureSeedCount <- seedDf %>% dplyr::count(feature)
featureOrthoCount <- orthoDf %>% dplyr::count(feature)
featureCount <- merge(
featureSeedCount, featureOrthoCount, by = "feature", all = TRUE
)
featureCount$type <- "unique"
featureCount$type[featureCount$n.x == featureCount$n.y] <- "shared"
if (ignoreInstanceNo == TRUE) {
featureCount$type[
!is.na(featureCount$n.x) & !is.na(featureCount$n.y)] <- "shared"
}
featureCount$feature <- as.character(featureCount$feature)
sharedFeatures <-unique(featureCount$feature[featureCount$type == "shared"])
uniqueFeatures <-unique(featureCount$feature[featureCount$type == "unique"])
allFeatures <- c(sharedFeatures, uniqueFeatures)
if (colorType == "Unique" & length(uniqueFeatures) == 0)
colorType <- "All"
if (colorType == "Shared" & length(sharedFeatures) == 0)
colorType <- "All"
if (colorType == "Unique") {
sharedFeaturesColors <- rep("#C9C9C9", length(sharedFeatures))
uniqueFeaturesColors <- getQualColForVector(uniqueFeatures)
if (checkColorPalette(uniqueFeatures, colorPalette) == TRUE) {
uniqueFeaturesColors <-
suppressWarnings(head(
RColorBrewer::brewer.pal(
length(uniqueFeatures), colorPalette),
length(uniqueFeatures)
))
}
allColors <- c(sharedFeaturesColors, uniqueFeaturesColors)
colorScheme <- data.frame(color = allColors, feature = allFeatures)
} else if (colorType == "Shared") {
sharedFeaturesColors <- getQualColForVector(sharedFeatures)
uniqueFeaturesColors <- rep("#C9C9C9", length(uniqueFeatures))
if (checkColorPalette(sharedFeatures, colorPalette) == TRUE) {
sharedFeaturesColors <-
suppressWarnings(head(
RColorBrewer::brewer.pal(
length(sharedFeatures), colorPalette),
length(sharedFeatures)
))
}
allColors <- c(sharedFeaturesColors, uniqueFeaturesColors)
colorScheme <- data.frame(color = allColors, feature = allFeatures)
} else if (colorType == "All") {
allColors <- getQualColForVector(allFeatures)
if (checkColorPalette(allFeatures, colorPalette) == TRUE) {
allColors <-
suppressWarnings(head(
RColorBrewer::brewer.pal(length(allFeatures), colorPalette),
length(allFeatures)
))
}
colorScheme <- data.frame(color = allColors, feature = allFeatures)
} else {
tmpDf <- data.frame(str_split_fixed(allFeatures, "_", 2))
tmpDf$name <- paste(tmpDf$X1, tmpDf$X2, sep = "_")
tmpDf$name[tmpDf$X2 == ""] <- tmpDf$X1[tmpDf$X2 == ""]
tmpDf$X2[tmpDf$X2 == ""] <- tmpDf$X1[tmpDf$X2 == ""]
typeColorDf <- data.frame(
colors = head(
suppressWarnings(RColorBrewer::brewer.pal(
nlevels(as.factor(tmpDf$X1)), colorPalette)),
nlevels(as.factor(tmpDf$X1))
),
X1 = levels(as.factor(tmpDf$X1))
)
tmpDf <- merge(tmpDf, typeColorDf, all.x = TRUE)
colorScheme <- data.frame(color = tmpDf$colors, feature = tmpDf$name)
}
# add color to seedDf and orthoDf
seedDf <- merge(seedDf, colorScheme, by = "feature", all.x = TRUE)
orthoDf <- merge(orthoDf, colorScheme, by = "feature", all.x = TRUE)
return(list(seedDf, orthoDf))
}
BIONF/PhyloProfile documentation built on Sept. 25, 2024, 4:46 p.m.
R Package Documentation
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Defines functions addFeatureColors linearizeArchitecture resolveOverlapFeatures checkOverlapDomains joinPlotMergeLegends modifyFeatureName sortDomainsByList sortDomains pairDomainPlotting singleDomainPlotting createArchiPlot
Documented in addFeatureColors checkOverlapDomains createArchiPlot joinPlotMergeLegends linearizeArchitecture modifyFeatureName pairDomainPlotting resolveOverlapFeatures singleDomainPlotting sortDomains sortDomainsByList
#' Create protein's domain architecure plot
#' @description Create architecture plot for both seed and orthologous protein.
#' If domains of ortholog are missing, only architecture of seed protein will
#' be plotted. NOTE: seed protein ID is the one being shown in the profile plot,
#' which normally is also the orthologous group ID.
#' @export
#' @usage createArchiPlot(info, domainDf, labelArchiSize, titleArchiSize,
#' showScore, showWeight, namePosition, firstDist, nameType, nameSize,
#' segmentSize, nameColor, labelPos, colorType, ignoreInstanceNo,
#' currentNCBIinfo, featureClassSort, featureClassOrder, colorPalette,
#' resolveOverlap, font)
#' @param info A list contains seed and ortholog's IDs
#' @param domainDf Dataframe contains domain info for the seed and ortholog.
#' This including the seed ID, orthologs IDs, sequence lengths, feature names,
#' start and end positions, feature weights (optional) and the status to
#' determine if that feature is important for comparison the architecture
#' between 2 proteins* (e.g. seed protein vs ortholog) (optional).
#' @param labelArchiSize Lable size (in px). Default = 12.
#' @param titleArchiSize Title size (in px). Default = 12.
#' @param showScore Show/hide E-values and Bit-scores. Default = NULL (hide)
#' @param showWeight Show/hide feature weights. Default = NULL (hide)
#' @param namePosition list of positions for domain names, choose from "plot",
#' "legend" or "axis". Default: "plot"
#' @param firstDist Distance of the first domain to plot title. Default = 0.5
#' @param nameType Type of domain names, either "Texts" or "Labels" (default)
#' @param nameSize Size of domain names. Default = 3
#' @param segmentSize Height of domain segment. Default = 5
#' @param nameColor Color of domain names (for Texts only). Default = "black"
#' @param labelPos Position of domain names (for Labels only). Choose from
#' @param colorType Choose to color "all", "shared", "unique" features or color
#' by "Feature type". Default = "all"
#' @param ignoreInstanceNo Ignore number of feature instances while identifying
#' shared or unique features. Default = FALSE
#' @param currentNCBIinfo Dataframe of the pre-processed NCBI taxonomy
#' data. Default = NULL (will be automatically retrieved from PhyloProfile app)
#' @param featureClassSort Choose to sort features. Default = "Yes"
#' @param featureClassOrder vector of ordered feature classes
#' @param colorPalette Choose between "Paired", "Set1", "Set2", "Set3",
#' "Accent", "Dark2" for the color pallete
#' @param resolveOverlap Choose to merge non-overlapped features of a feature
#' type into one line. Default = "Yes"
#' @param font font of text. Default = Arial"
#' @return A domain plot as arrangeGrob object. Use grid::grid.draw(plot) to
#' render.
#' @author Vinh Tran tran@bio.uni-frankfurt.de
#' @importFrom stringr str_count
#' @seealso \code{\link{singleDomainPlotting}},\code{\link{pairDomainPlotting}},
#' \code{\link{sortDomains}}, \code{\link{parseDomainInput}}
#' @examples
#' seedID <- "101621at6656"
#' orthoID <- "101621at6656|AGRPL@224129@0|224129_0:001955|1"
#' info <- c(seedID, orthoID)
#' domainFile <- system.file(
#' "extdata", "domainFiles/101621at6656.domains",
#' package = "PhyloProfile", mustWork = TRUE
#' )
#' domainDf <- parseDomainInput(seedID, domainFile, "file")
#' domainDf$feature_id_mod <- domainDf$feature_id
#' domainDf$feature_id_mod <- gsub("SINGLE", "LCR", domainDf$feature_id_mod)
#' domainDf$feature_id_mod[domainDf$feature_type == "coils"] <- "Coils"
#' domainDf$feature_id_mod[domainDf$feature_type == "seg"] <- "LCR"
#' domainDf$feature_id_mod[domainDf$feature_type == "tmhmm"] <- "TM"
#' plot <- createArchiPlot(info, domainDf, font = "sans")
#' grid::grid.draw(plot)
createArchiPlot <- function(
info = NULL, domainDf = NULL, labelArchiSize = 12, titleArchiSize = 12,
showScore = NULL, showWeight = NULL, namePosition = "plot",
firstDist = 0.5, nameType = "Labels", nameSize = 3, segmentSize = 5,
nameColor = "#000000", labelPos = "Above", colorType = "Unique",
ignoreInstanceNo = FALSE, currentNCBIinfo = NULL,
featureClassSort = "Yes", featureClassOrder = NULL,
colorPalette = "Paired", resolveOverlap = "Yes", font = "Arial"
){
if (is.null(info) | is.null(domainDf)) return(ggplot() + theme_void())
group <- as.character(info[1])
ortho <- as.character(info[2])
# get sub dataframe based on selected groupID and orthoID
group <- gsub("\\|", ":", group)
ortho <- gsub("\\|", ":", ortho)
grepID <- paste(group, "#", ortho, sep = "")
subdomainDf <- domainDf
subdomainDf$feature <- as.character(subdomainDf$feature)
subdomainDf <- subdomainDf[!duplicated(subdomainDf), ]
orthoID <- NULL
if (nrow(subdomainDf) < 1) return(paste0("No domain info available!"))
else {
# get minStart and maxEnd
minStart <- min(subdomainDf$start)
maxEnd <- max(subdomainDf$end)
if ("length" %in% colnames(subdomainDf))
maxEnd <- max(c(subdomainDf$end, subdomainDf$length))
# ortho & seed domains df
orthoDf <- subdomainDf[subdomainDf$orthoID == ortho,]
seedDf <- subdomainDf[subdomainDf$orthoID != ortho,]
if (nrow(seedDf) == 0) seedDf <- orthoDf
seed <- as.character(seedDf$orthoID[1])
if (nrow(seedDf) == 0) return(paste0("No domain info available!"))
# simplify seed/ortho seq IDs if they are in bionf format
if (!is.null(currentNCBIinfo)) {
if (
stringr::str_count(seed, ":") >= 2 &
stringr::str_count(seed, "@") >= 2
) {
seedTmp <- strsplit(as.character(seed),':', fixed = TRUE)[[1]]
seedSpec <-
strsplit(as.character(seedTmp[2]),'@', fixed = TRUE)[[1]][2]
seed <- paste0(
id2name(seedSpec, currentNCBIinfo)[,2], " - ", seedTmp[3]
)
if (ortho != seed) {
orthoTmp <- strsplit(
as.character(ortho),':', fixed = TRUE)[[1]]
orthoSpec <-
strsplit(
as.character(orthoTmp[2]),'@',fixed = TRUE)[[1]][2]
ortho <- paste0(
id2name(orthoSpec, currentNCBIinfo)[,2],
" - ", orthoTmp[3]
)
}
}
}
# add feature colors
featureColorDf <- addFeatureColors(
seedDf, orthoDf, colorType, colorPalette, ignoreInstanceNo
)
seedDf <- featureColorDf[[1]]
orthoDf <- featureColorDf[[2]]
# resolve (non)overlapped features
if (resolveOverlap == "Yes") {
seedDf <- resolveOverlapFeatures(seedDf)
orthoDf <- resolveOverlapFeatures(orthoDf)
} else {
seedDf$featureOri <- seedDf$feature
seedDf$featureOri <- as.character(seedDf$featureOri)
orthoDf$featureOri <- orthoDf$feature
orthoDf$featureOri <- as.character(orthoDf$featureOri)
}
if (nrow(orthoDf) > 0) {
if (all.equal(seedDf, orthoDf)[1] == TRUE) featureClassSort <- "No"
# sort features
if (featureClassSort == "Yes") {
# change order of one df's features based on order of other df's
if (length(orthoDf$feature) < length(seedDf$feature)) {
orderedOrthoDf <- orthoDf[order(orthoDf$feature), ]
orderedSeedDf <- sortDomains(orderedOrthoDf, seedDf)
orderedOrthoDf <- sortDomains(orderedSeedDf, orderedOrthoDf)
} else {
orderedSeedDf <- seedDf[order(seedDf$feature), ]
orderedOrthoDf <- sortDomains(orderedSeedDf, orthoDf)
orderedSeedDf <- sortDomains(orderedOrthoDf, orderedSeedDf)
}
} else {
# change order based on list of feature types
orderedSeedDf <- sortDomainsByList(seedDf, featureClassOrder)
orderedOrthoDf <- sortDomainsByList(orthoDf, featureClassOrder)
}
# plotting
g <- pairDomainPlotting(
seed, ortho, orderedSeedDf, orderedOrthoDf, minStart, maxEnd,
labelArchiSize, titleArchiSize, showScore, showWeight,
namePosition, firstDist, nameType, nameSize, segmentSize,
nameColor, labelPos, colorPalette, font)
} else {
orderedSeedDf <- sortDomainsByList(seedDf, featureClassOrder)
# plotting
g <- pairDomainPlotting(
seed, seed, orderedSeedDf, orderedSeedDf, minStart, maxEnd,
labelArchiSize, titleArchiSize, showScore, showWeight,
namePosition, firstDist, nameType, nameSize, segmentSize,
nameColor, labelPos, colorPalette, font)
}
return(g)
}
}
#' Create architecure plot for a single protein
#' @usage singleDomainPlotting(df, geneID, sep, labelSize, titleSize, minStart,
#' maxEnd, colorPalette, showScore, showWeight, namePosition, firstDist,
#' nameType, nameSize, segmentSize, nameColor, labelPos, font)
#' @param df Domain dataframe for ploting containing the seed ID, ortholog ID,
#' ortholog sequence length, feature names, start and end positions,
#' feature weights (optional) and the status to determine if that feature is
#' important for comparison the architecture between 2 proteins* (e.g. seed
#' protein vs ortholog) (optional)
#' @param geneID ID of seed or orthologous protein
#' @param sep Separate indicator for title. Default = "|"
#' @param labelSize Lable size. Default = 12
#' @param titleSize Title size. Default = 12
#' @param minStart The smallest start position of all domains
#' @param maxEnd The highest stop position of all domains
#' @param colorPalette Color pallete. Default = Paired"
#' @param showScore Show/hide E-values and Bit-scores. Default = NULL (hide)
#' @param showWeight Show/hide feature weights. Default = NULL (hide)
#' @param namePosition List of positions for domain names, choose from "plot",
#' "legend" or "axis". Default: "plot"
#' @param firstDist Distance of the first domain to plot title. Default = 0.5
#' @param nameType Type of domain names, either "Texts" or "Labels" (default)
#' @param nameSize Size of domain names. Default = 3
#' @param segmentSize Height of domain segment. Default = 5
#' @param nameColor Color of domain names (for Texts only). Default = "black"
#' @param labelPos Position of domain names (for Labels only). Choose from
#' "Above" (default), "Below" or "Inside" the domain bar
#' @param font font of text. Default = Arial"
#' @return Domain plot of a single protein as a ggplot object.
#' @author Vinh Tran tran@bio.uni-frankfurt.de
#' @importFrom RColorBrewer brewer.pal
#' @importFrom stringr str_wrap
#' @seealso \code{\link{parseDomainInput}}
#' @import ggplot2
#' @examples
#' seed <- "101621at6656"
#' ortho <- "101621at6656|AGRPL@224129@0|224129_0:001955|1"
#' ortho <- gsub("\\|", ":", ortho)
#' grepID <- paste(seed, "#", ortho, sep = "")
#' domainFile <- system.file(
#' "extdata", "domainFiles/101621at6656.domains",
#' package = "PhyloProfile", mustWork = TRUE
#' )
#' domainDf <- parseDomainInput(seed, domainFile, "file")
#' domainDf$feature_id_mod <- domainDf$feature_id
#' subdomainDf <- domainDf[grep(grepID, domainDf$seedID), ]
#' subdomainDf$feature <- as.character(subdomainDf$feature)
#' orthoDf <- subdomainDf[subdomainDf$orthoID == ortho,]
#' seedDf <- subdomainDf[subdomainDf$orthoID != ortho,]
#' minStart <- min(subdomainDf$start)
#' maxEnd <- max(c(subdomainDf$end, subdomainDf$length))
#' # resolve overlapping domains
#' seedDf <- PhyloProfile:::resolveOverlapFeatures(seedDf)
#' orthoDf <- PhyloProfile:::resolveOverlapFeatures(orthoDf)
#' # add feature colors
#' featureColorDf <- PhyloProfile:::addFeatureColors(seedDf, orthoDf)
#' seedDf <- featureColorDf[[1]]
#' orthoDf <- featureColorDf[[2]]
#' # do plot
#' g <- PhyloProfile:::singleDomainPlotting(
#' seedDf, seed, minStart = minStart, maxEnd = maxEnd, font = "sans"
#' )
#' grid::grid.draw(g)
singleDomainPlotting <- function(
df = NULL, geneID = "GeneID", sep = "|", labelSize = 12, titleSize = 12,
minStart = NULL, maxEnd = NULL, colorPalette = "Set2",
showScore = NULL, showWeight = NULL, namePosition = "plot",
firstDist = 0.5, nameType = "Labels", nameSize = 3, segmentSize = 5,
nameColor = "#000000", labelPos = "Above", font = "Arial"
){
feature <- feature_id_mod <- end <- start <- featureOri <- NULL
evalue <- bitscore <- weight <- NULL
# parse parameters
if (is.null(df)) return(ggplot() + theme_void())
if (is.null(minStart)) minStart <- min(df$start)
if (is.null(maxEnd)) maxEnd <- max(df$end)
if ("color" %in% colnames(df)) {
colorScheme <- structure(
df$color, .Names = df$featureOri
)
} else {
colorScheme <- structure(
head(
suppressWarnings(
RColorBrewer::brewer.pal(
nlevels(as.factor(df$feature)), colorPalette
)
),
levels(as.factor(df$feature))
),
.Names = levels(as.factor(df$feature)))
}
# initiate ggplot object
gg <- ggplot(df, aes(y = feature, x = end))
# draw lines for representing sequence length
if ("length" %in% colnames(df)) {
gg <- gg + geom_segment(
data = df, linewidth = 0.6, color = "#b2b2b2", alpha = 0.5,
aes(x = 0, xend = length, y = feature, yend = feature))
}
# draw features
gg <- gg + geom_segment(
data = df, aes(
x = start, xend = end, y = feature, yend = feature,
color = as.factor(featureOri)
), linewidth = segmentSize, alpha = 1.0) +
scale_color_manual(values = colorScheme)
# add feature names
if ("plot" %in% namePosition) {
if (nameType == "Labels") {
if (labelPos == "Above") {
gg <- gg + geom_label(
aes(
label = stringr::str_wrap(feature_id_mod),
x = (start+end)/2
),
color = "black", vjust = -0.5, size = nameSize, family=font
)
} else if (labelPos == "Below") {
gg <- gg + geom_label(
aes(
label = stringr::str_wrap(feature_id_mod),
x = (start+end)/2
),
color = "black", vjust = 1.5, size = nameSize, family = font
)
} else {
gg <- gg + geom_label(
aes(
label = stringr::str_wrap(feature_id_mod),
x = (start+end)/2
),
color = "black", size = nameSize, family = font
)
}
} else {
gg <- gg + geom_text(
aes(
label = stringr::str_wrap(feature_id_mod),
x = (start+end)/2
),
color = nameColor, check_overlap = TRUE, size = nameSize,
family = font
)
}
}
# add scores if selected
if ("Bit-score" %in% showScore & "E-value" %in% showScore) {
gg <- gg + geom_label(
aes(
label = ifelse(
evalue == "NA" & bitscore == "NA", "", stringr::str_wrap(
paste0("E-value: ", evalue, "; Bitscore: ", bitscore)
)
), x = (start+end)/2
), color = "black", vjust = 1.25
)
} else if ("Bit-score" %in% showScore) {
gg <- gg + geom_label(
aes(
label = ifelse(bitscore == "NA", "", stringr::str_wrap(
paste0("Bitscore: ", bitscore)
)), x = (start+end)/2
), color = "black", vjust = 1.25
)
} else if ("E-value" %in% showScore) {
gg <- gg + geom_label(
aes(
label = ifelse(evalue == "NA", "", stringr::str_wrap(
paste0("E-value: ", evalue)
)), x = (start+end)/2
), color = "black", vjust = 1.25
)
}
# add weight if selected
if ("Weight" %in% showWeight) {
vjustValue <- 1.25
if ("E-value" %in% showScore | "Bit-score" %in% showScore)
vjustValue <- 2.25
gg <- gg + geom_label(
aes(
label = ifelse(weight == "NA", "", stringr::str_wrap(
paste0("Weight: ", weight)
)), x = (start+end)/2
), color = "black", vjust = vjustValue
)
}
# theme format
gg <- gg + labs(
title = paste0(gsub(":", sep, geneID)), color = "Feature"
)
gg <- gg + theme(
axis.line = element_blank(), axis.ticks.y = element_blank(),
panel.grid.minor.x=element_blank(), panel.grid.major.x=element_blank(),
panel.background = element_blank()
)
gg <- gg + theme(
plot.title = element_text(face = "bold", size = titleSize, hjust = 0.5)
)
gg <- gg + theme(
axis.title = element_blank(),
axis.text.x = element_text(size = labelSize))
gg <- gg + theme(text = element_text(family = font))
# add feature names on the axis (if required)
if ("axis" %in% namePosition) {
if ("plot" %in% namePosition | "legend" %in% namePosition) {
gg <- gg + scale_y_discrete(
expand = c(0.075, 0), breaks = df$feature,
labels = df$feature_type)
} else {
gg <- gg + scale_y_discrete(
expand = c(0.075, 0), breaks = df$feature, labels = df$feature)
}
gg <- gg + theme(axis.text.y = element_text(size = labelSize))
} else {
gg <- gg + theme(axis.text.y = element_blank())
}
# add legend (if required)
if ("legend" %in% namePosition) {
gg <- gg + theme(legend.position = "bottom")
} else {
gg <- gg + theme(legend.position = "none")
}
# add space on the top of the plot (for feature name)
gg <- gg + coord_cartesian(
clip = 'off', ylim = c(1, nlevels(as.factor(df$feature)) + firstDist)
)
# scale x-axis to the length of the longest protein
gg <- gg + xlim(0, maxEnd)
return(gg)
}
#' Create architecure plot for a pair of seed and ortholog protein
#' @usage pairDomainPlotting(seed, ortho, seedDf, orthoDf, minStart, maxEnd,
#' labelSize, titleSize, showScore, showWeight, namePosition, firstDist,
#' nameType, nameSize, segmentSize, nameColor, labelPos, colorPalette, font)
#' @param seed Seed ID
#' @param ortho Ortho ID
#' @param seedDf domain dataframe for seed domains containing the seed ID,
#' ortholog ID, sequence length, feature names, start and end positions,
#' feature weights (optional) and the status to determine if that feature is
#' important for comparison the architecture between 2 proteins* (e.g. seed
#' protein vs ortholog) (optional)
#' @param orthoDf domain dataframe for ortholog domains (same format as seedDf)
#' @param minStart the smallest start position of all domains
#' @param maxEnd the highest stop position of all domains
#' @param labelSize lable size. Default = 12
#' @param titleSize title size. Default = 12
#' @param showScore show/hide E-values and Bit-scores. Default = NULL (hide)
#' @param showWeight Show/hide feature weights. Default = NULL (hide)
#' @param namePosition list of positions for domain names, choose from "plot",
#' "legend" or "axis". Default: "plot"
#' @param firstDist distance of the first domain to plot title. Default = 0.5
#' @param nameType type of domain names, either "Texts" or "Labels" (default)
#' @param nameSize Size of domain names. Default = 3
#' @param segmentSize Height of domain segment. Default = 5
#' @param nameColor color of domain names (for Texts only). Default = "black"
#' @param labelPos position of domain names (for Labels only). Choose from
#' "Above" (default), "Below" or "Inside" the domain bar
#' @param colorPalette color pallete. Default = Paired"
#' @param font font of text. Default = Arial"
#' @return Domain plot of a pair proteins as a arrangeGrob object.
#' @author Vinh Tran tran@bio.uni-frankfurt.de
#' @importFrom gridExtra grid.arrange
#' @seealso \code{\link{singleDomainPlotting}}, \code{\link{sortDomains}},
#' \code{\link{parseDomainInput}}
#' @examples
#' seed <- "101621at6656"
#' ortho <- "101621at6656|AGRPL@224129@0|224129_0:001955|1"
#' ortho <- gsub("\\|", ":", ortho)
#' grepID <- paste(seed, "#", ortho, sep = "")
#' domainFile <- system.file(
#' "extdata", "domainFiles/101621at6656.domains",
#' package = "PhyloProfile", mustWork = TRUE
#' )
#' domainDf <- parseDomainInput(seed, domainFile, "file")
#' domainDf$feature_id_mod <- domainDf$feature_id
#' subdomainDf <- domainDf[grep(grepID, domainDf$seedID), ]
#' subdomainDf$feature <- as.character(subdomainDf$feature)
#' orthoDf <- subdomainDf[subdomainDf$orthoID == ortho,]
#' seedDf <- subdomainDf[subdomainDf$orthoID != ortho,]
#' minStart <- min(subdomainDf$start)
#' maxEnd <- max(c(subdomainDf$end, subdomainDf$length))
#' # resolve overlapping domains
#' seedDf <- PhyloProfile:::resolveOverlapFeatures(seedDf)
#' orthoDf <- PhyloProfile:::resolveOverlapFeatures(orthoDf)
#' # add feature colors
#' featureColorDf <- PhyloProfile:::addFeatureColors(seedDf, orthoDf)
#' seedDf <- featureColorDf[[1]]
#' orthoDf <- featureColorDf[[2]]
#' # do plot
#' g <- PhyloProfile:::pairDomainPlotting(
#' seed,ortho,seedDf,orthoDf,minStart,maxEnd, font = "sans"
#' )
#' grid::grid.draw(g)
pairDomainPlotting <- function(
seed = NULL, ortho = NULL, seedDf = NULL, orthoDf = NULL,
minStart = 0, maxEnd = 999, labelSize = 12, titleSize = 12,
showScore = NULL, showWeight = NULL, namePosition = "plot",
firstDist = 0.5, nameType = "Labels", nameSize = 3, segmentSize = 5,
nameColor = "#000000", labelPos = "Above", colorPalette = "Paired",
font = "Arial"
) {
if(is.null(seed) | is.null(ortho) | is.null(seedDf) | is.null(orthoDf))
stop("Seed/Ortho ID or domain dataframe is NULL!")
sep <- "|"
plotSeed <- singleDomainPlotting(
seedDf, seed, sep, labelSize, titleSize, minStart, maxEnd, colorPalette,
showScore, showWeight, namePosition, firstDist, nameType, nameSize,
segmentSize, nameColor, labelPos, font
)
if (ortho == seed) {
g <- plotSeed
} else {
plotOrtho <- singleDomainPlotting(
orthoDf, ortho, sep, labelSize, titleSize, minStart, maxEnd,
colorPalette, showScore, showWeight, namePosition, firstDist,
nameType, nameSize, segmentSize, nameColor, labelPos, font
)
if ("legend" %in% namePosition) {
g <- joinPlotMergeLegends(
seedDf, orthoDf, plotSeed, plotOrtho, position = "bottom", font
)
} else {
seedHeight <- length(levels(as.factor(seedDf$feature)))
orthoHeight <- length(levels(as.factor(orthoDf$feature)))
g <- gridExtra::grid.arrange(
plotSeed, plotOrtho, nrow = 2,
heights = c(seedHeight, orthoHeight)
)
}
}
return(g)
}
#' Sort one domain dataframe based on the other domain dataframe
#' @description Sort domain dataframe of one protein (either seed or ortholog)
#' based on the dataframe of the its paired protein, in order to bring the
#' common domain feature in the same order which make it easy for comparing.
#' @param seedDf data of seed protein
#' @param orthoDf data of ortholog protein
#' @return Dataframe contains sorted domain list.
#' @author Vinh Tran tran@bio.uni-frankfurt.de
#' @examples
#' # get domain data
#' seedID <- "101621at6656"
#' domainFile <- system.file(
#' "extdata", "domainFiles/101621at6656.domains",
#' package = "PhyloProfile", mustWork = TRUE
#' )
#' domainDf <- parseDomainInput(seedID, domainFile, "file")
#' # get seedDf and orthoDf
#' subDf <- domainDf[
#' domainDf$seedID ==
#' "101621at6656#101621at6656:AGRPL@224129@0:224129_0:001955:1",]
#' orthoDf <- subDf[subDf$orthoID == "101621at6656:DROME@7227@1:Q9VG04",]
#' seedDf <- subDf[subDf$orthoID != "101621at6656:DROME@7227@1:Q9VG04",]
#' # sort
#' PhyloProfile:::sortDomains(seedDf, orthoDf)
sortDomains <- function(seedDf, orthoDf){
if (is.null(seedDf) | is.null(orthoDf))
stop("Domain data for seed & ortholog cannot be NULL!")
orderNo <- NULL
# get list of features in seedDf
featureList <- as.data.frame(levels(as.factor(seedDf$feature)))
colnames(featureList) <- c("feature")
# and add order number to each feature
featureList$orderNo <- seq(length(featureList$feature))
# merge those info to orthoDf
orderedOrthoDf <- merge(orthoDf, featureList, all.x = TRUE)
# sort orthoDf
index <- with(orderedOrthoDf, order(orderNo))
orderedOrthoDf <- orderedOrthoDf[index, ]
# convert feature column into a character vector
orderedOrthoDf$feature <- as.character(orderedOrthoDf$feature)
# then convert it back into an ordered factor
# (to keep this order when plotting)
orderedOrthoDf$feature <- factor(
orderedOrthoDf$feature, levels = unique(orderedOrthoDf$feature)
)
# return sorted df
return(orderedOrthoDf)
}
#' Sort one domain dataframe based on list of ordered feature types
#' @description Sort domain dataframe of one protein based on a given list of
#' ordered feature types
#' @param domainDf domain dataframe
#' @param featureClassOrder vector of ordered feature classes
#' @return Dataframe contains sorted domain list.
#' @author Vinh Tran tran@bio.uni-frankfurt.de
#' @importFrom dplyr left_join
#' @examples
#' # get domain data
#' seedID <- "101621at6656"
#' domainFile <- system.file(
#' "extdata", "domainFiles/101621at6656.domains",
#' package = "PhyloProfile", mustWork = TRUE
#' )
#' domainDf <- parseDomainInput(seedID, domainFile, "file")
#' # get seedDf and orthoDf
#' subDf <- domainDf[
#' domainDf$seedID ==
#' "101621at6656#101621at6656:AGRPL@224129@0:224129_0:001955:1",]
#' orthoDf <- subDf[subDf$orthoID == "101621at6656:DROME@7227@1:Q9VG04",]
#' featureClassOrder <- c("pfam", "smart", "tmhmm", "coils", "signalp", "seg",
#' "flps")
#' # sort
#' PhyloProfile:::sortDomainsByList(orthoDf, featureClassOrder)
sortDomainsByList <- function(domainDf = NULL, featureClassOrder = NULL) {
if (is.null(domainDf) | is.null(featureClassOrder))
stop("Domain data or feature type order is NULL!")
featureClassOrder <- rev(featureClassOrder[
featureClassOrder %in% levels(as.factor(domainDf$feature_type))
])
orderedDomainDf <- dplyr::left_join(
data.frame(feature_type = featureClassOrder),
domainDf, by = "feature_type"
)
orderedDomainDf$feature <- factor(
orderedDomainDf$feature, levels = unique(orderedDomainDf$feature)
)
return(orderedDomainDf)
}
#' Modify feature names
#' @description Simplify feature names (e.g. TM for transmembrane domain,
#' LCR for low complexity regions, remove tool names from domain name) and add
#' weight to feature names (if available)
#' @param domainDf domain data as a dataframe object
#' @return Dataframe contains simlified domain names in yLabel column
#' @author Vinh Tran tran@bio.uni-frankfurt.de
#' @examples
#' domainFile <- system.file(
#' "extdata", "domainFiles/101621at6656.domains",
#' package = "PhyloProfile", mustWork = TRUE
#' )
#' seedID <- "101621at6656"
#' domainDf <- parseDomainInput(seedID, domainFile, "file")
#' PhyloProfile:::modifyFeatureName(domainDf)
modifyFeatureName <- function(domainDf = NULL) {
if (is.null(domainDf)) stop("Domain data cannot be NULL!")
domainDf$yLabel <- domainDf$feature_id
domainDf$yLabel[domainDf$yLabel == "transmembrane"] <- "TM"
domainDf$yLabel[domainDf$yLabel == "low complexity regions"] <- "LCR"
domainDf$yLabel[domainDf$yLabel == "low_complexity_regions"] <- "LCR"
return(domainDf)
}
#' Join multiple plots and merge legends
#' @param df1 Data frame for plot 1
#' @param df2 Data frame for plot 2
#' @param plot1 ggplot object of plot 1
#' @param plot2 ggplot object of plot 2
#' @param position position of legend (bottom or right)
#' @param font font of text
#' @return joined plots with merged legend as a grid object
#' @author Vinh Tran tran@bio.uni-frankfurt.de
#' @importFrom gridExtra grid.arrange
#' @examples
#' seed <- "101621at6656"
#' ortho <- "101621at6656|AGRPL@224129@0|224129_0:001955|1"
#' ortho <- gsub("\\|", ":", ortho)
#' grepID <- paste(seed, "#", ortho, sep = "")
#' domainFile <- system.file(
#' "extdata", "domainFiles/101621at6656.domains",
#' package = "PhyloProfile", mustWork = TRUE
#' )
#' domainDf <- parseDomainInput(seed, domainFile, "file")
#' domainDf$feature_id_mod <- domainDf$feature_id
#' subdomainDf <- domainDf[grep(grepID, domainDf$seedID), ]
#' subdomainDf$feature <- as.character(subdomainDf$feature)
#' orthoDf <- subdomainDf[subdomainDf$orthoID == ortho,]
#' seedDf <- subdomainDf[subdomainDf$orthoID != ortho,]
#' minStart <- min(subdomainDf$start)
#' maxEnd <- max(c(subdomainDf$end, subdomainDf$length))
#' # resolve overlapping domains
#' seedDf <- PhyloProfile:::resolveOverlapFeatures(seedDf)
#' orthoDf <- PhyloProfile:::resolveOverlapFeatures(orthoDf)
#' # add feature colors
#' featureColorDf <- PhyloProfile:::addFeatureColors(seedDf, orthoDf)
#' seedDf <- featureColorDf[[1]]
#' orthoDf <- featureColorDf[[2]]
#' # generate plots
#' plotSeed <- PhyloProfile:::singleDomainPlotting(
#' seedDf, seed, minStart = minStart, maxEnd = maxEnd, font = "sans"
#' )
#' plotOrtho <- PhyloProfile:::singleDomainPlotting(
#' orthoDf, ortho, minStart = minStart, maxEnd = maxEnd, font = "sans"
#' )
#' # merge plots
#' PhyloProfile:::joinPlotMergeLegends(
#' seedDf, orthoDf, plotSeed, plotOrtho, "bottom", font = "sans")
joinPlotMergeLegends <- function(
df1 = NULL, df2 = NULL, plot1 = NULL, plot2 = NULL,
position = c("bottom", "right"), font = "Arial")
{
if (is.null(plot1) | is.null(df1)) stop("No plot data given!")
if (is.null(plot2) | is.null(df2))
return(plot1 + theme(legend.position = position))
featureOri <- NULL
# remove legend of the original plots
plot1 <- plot1 + theme(legend.position = "none")
plot2 <- plot2 + theme(legend.position = "none")
# combine plot1 and 2
combined_plot <- gridExtra::grid.arrange(
plot1, plot2, ncol = 1,
heights = c(
length(levels(as.factor(df1$feature))),
length(levels(as.factor(df2$feature)))
)
)
# create a temp plot that contains all features
mergedDf <- rbind(df1, df2)
colorScheme <- structure(
mergedDf$color, .Names = mergedDf$featureOri
)
tmpPlot <- ggplot() +
geom_segment(
data = mergedDf,
aes(
x = 0, xend = 1, y = 1, yend = 1,
color = featureOri
),
linewidth = 5, lineend = "round", alpha = 0.7
) +
scale_color_manual(values = colorScheme) +
labs(color = "Feature") +
theme_minimal() +
theme(legend.position = position, text = element_text(family = font))
# extract legend from the temp plot above
getOnlyLegend <- function(plot) {
plotTable <- ggplot_gtable(ggplot_build(plot))
legendPlot <- which(
vapply(
plotTable$grobs, function(x) x$name, character(1)
) == "guide-box"
)
legend <- plotTable$grobs[[legendPlot]]
return(legend)
}
legend <- getOnlyLegend(tmpPlot)
# final combined plot with shared legend
combined <- gridExtra::grid.arrange(
combined_plot, legend, nrow = 2, heights = c(10, 1)
)
return(combined)
}
#' Identify feature type(s) containing overlapped domains/features
#' @param domainDf input domain dataframe
#' @return List of feature types that have overlapped domains
#' @author Vinh Tran tran@bio.uni-frankfurt.de
#' @importFrom dplyr group_by add_count
#' @examples
#' # get domain data
#' seedID <- "101621at6656"
#' domainFile <- system.file(
#' "extdata", "domainFiles/101621at6656.domains",
#' package = "PhyloProfile", mustWork = TRUE
#' )
#' domainDf <- parseDomainInput(seedID, domainFile, "file")
#' # get seedDf and orthoDf
#' subDf <- domainDf[
#' domainDf$seedID ==
#' "101621at6656#101621at6656:AGRPL@224129@0:224129_0:001955:1",]
#' orthoDf <- subDf[subDf$orthoID == "101621at6656:DROME@7227@1:Q9VG04",]
#' # check overlap features
#' PhyloProfile:::checkOverlapDomains(orthoDf)
checkOverlapDomains <- function(domainDf) {
if (is.null(domainDf)) stop("Domain data cannot be NULL!")
feature_type <- NULL
df <- domainDf[, c("feature", "feature_type", "start", "end")]
df <- data.frame(
df %>% dplyr::group_by(feature_type) %>% dplyr::add_count(feature_type)
)
df$tmp <- paste(df$feature_type, df$end, sep = "_")
overlappedType <- lapply(
df$tmp[df$n > 1],
function (x) {
if (length(df$feature[df$tmp == x]) > 1)
return(df$feature_type[df$tmp == x])
ed <- df$end[df$tmp == x][1]
st <- df$start[df$tmp == x][1]
type <- df$feature_type[df$tmp == x][1]
subDf <- df[
!(df$tmp == x) & df$feature_type == type &
df$start < ed & df$end > st,
]
if (nrow(subDf) > 0) {
if(!(subDf$feature[1] == df$feature[df$tmp == x]))
return(subDf$feature_type)
}
}
)
return(unique(unlist(overlappedType)))
}
#' Modify domain dataframe to resolve overlapped domains/features
#' @param domainDf input domain dataframe
#' @return Domain dataframe with modified feature names that join multiple
#' domains of the same type that are not overlapped
#' @author Vinh Tran tran@bio.uni-frankfurt.de
#' @examples
#' # get domain data
#' seedID <- "101621at6656"
#' domainFile <- system.file(
#' "extdata", "domainFiles/101621at6656.domains",
#' package = "PhyloProfile", mustWork = TRUE
#' )
#' domainDf <- parseDomainInput(seedID, domainFile, "file")
#' # get seedDf and orthoDf
#' subDf <- domainDf[
#' domainDf$seedID ==
#' "101621at6656#101621at6656:AGRPL@224129@0:224129_0:001955:1",]
#' orthoDf <- subDf[subDf$orthoID == "101621at6656:DROME@7227@1:Q9VG04",]
#' # resolve overlapped featuers
#' PhyloProfile:::resolveOverlapFeatures(orthoDf)
resolveOverlapFeatures <- function(domainDf) {
if (is.null(domainDf)) stop("Domain data cannot be NULL!")
overlappedType <- checkOverlapDomains(domainDf)
domainDf$featureOri <- domainDf$feature
domainDf$featureOri <- as.character(domainDf$featureOri)
if (length(overlappedType) > 0) {
domainDf$feature <- ifelse(
!(domainDf$feature_type %in% overlappedType),
domainDf$feature_type,
domainDf$feature
)
} else {
domainDf$feature <- domainDf$feature_type
}
return(domainDf)
}
#' Linearize PFAM/SMART annotations by best e-value/bitscore
#' @export
#' @param domainDf input domain dataframe
#' @param orthoID ID of protein that needs to be linearized
#' @param value type of values that will be used for linearized, either evalue
#' (default) or bitscore
#' @return Domain dataframe of the selected protein after linearization
#' @author Vinh Tran tran@bio.uni-frankfurt.de
#' @importFrom dplyr arrange
#' @examples
#' demoDomainDf <- data.frame(
#' orthoID = rep("protID", 4),
#' start = c(1, 5, 100, 80),
#' end = c(30, 40, 130, 110),
#' evalue = c(0.001, 0.0005, 0.2, 0.004),
#' feature_type = c(rep("pfam", 2), rep("smart", 2)),
#' feature_id = c("pf1", "pf2", "sm1", "sm2")
#' )
#' linearizeArchitecture(demoDomainDf, "protID", "evalue")
linearizeArchitecture <- function(
domainDf = NULL, orthoID = NULL, value = "evalue"
) {
if (is.null(domainDf) | is.null(orthoID)) stop("Input data is NULL!")
evalue <- bitscore <- start <- end <- NULL
# Sort the dataframe by start position and then by evalue or bitscore
if (value == "evalue") {
domainDf <- domainDf %>% dplyr::arrange(start, evalue)
} else if (value == "bitscore") {
domainDf <- domainDf %>% dplyr::arrange(start, bitscore)
} else stop("Incorrect value specified! Either 'evalue' or 'bitscore'")
# Get lines that need to be excluded
pfamRows <- rownames(domainDf[domainDf$orthoID == orthoID &
domainDf$feature_type %in% c("pfam","smart"),])
exclude_lines <- vapply(
seq_len(length(pfamRows)-1),
function(i) {
if (domainDf[pfamRows[i],]$end >= domainDf[pfamRows[i+1],]$start) {
# Exclude the row with the higher evalue / lower bitscore
if (value == "evalue") {
if (
domainDf[pfamRows[i],]$evalue >
domainDf[pfamRows[i+1],]$evalue
) {
return((pfamRows[i]))
} else {
return((pfamRows[i+1]))
}
} else {
if (
domainDf[pfamRows[i],]$bitscore <
domainDf[pfamRows[i+1],]$bitscore
) {
return((pfamRows[i]))
} else {
return((pfamRows[i+1]))
}
}
} else {
return("0")
}
},
character(1)
)
# return domainDf after removing overlapped features with higher e-values
outDf <- domainDf[!(row.names(domainDf) %in% exclude_lines), ]
return(outDf[outDf$orthoID == orthoID,])
}
#' Add colors for each feature/domain
#' @description Add colors to features/domains of 2 domain dataframes. Users can
#' choose to color only the shared features, unique features, all features
#' (default) or based on feature types. Default color pallete is "Paired", but
#' it can be changed.
#' @param seedDf Domain dataframe of seed protein (protein 1)
#' @param orthoDf Domain dataframe of orthologs protein (protein 2)
#' @param colorType Choose to color "all", "shared", "unique" features or color
#' by "Feature type". Default: "all"
#' @param colorPalette Choose between "Paired", "Set1", "Set2", "Set3",
#' "Accent", "Dark2" for the color pallete
#' @param ignoreInstanceNo Ignore number of feature instances while identifying
#' shared or unique features. Default: FALSE
#' @return 2 dataframes (seedDf and orthoDf) with an additional column for the
#' assigned color to each feature instance
#' @author Vinh Tran tran@bio.uni-frankfurt.de
#' @importFrom RColorBrewer brewer.pal
#' @importFrom utils head
#' @importFrom dplyr count
#' @examples
#' # get domain data
#' seedID <- "101621at6656"
#' domainFile <- system.file(
#' "extdata", "domainFiles/101621at6656.domains",
#' package = "PhyloProfile", mustWork = TRUE
#' )
#' domainDf <- parseDomainInput(seedID, domainFile, "file")
#' # get seedDf and orthoDf
#' subDf <- domainDf[
#' domainDf$seedID ==
#' "101621at6656#101621at6656:AGRPL@224129@0:224129_0:001955:1",]
#' orthoDf <- subDf[subDf$orthoID == "101621at6656:DROME@7227@1:Q9VG04",]
#' seedDf <- subDf[subDf$orthoID != "101621at6656:DROME@7227@1:Q9VG04",]
#' # add colors to features
#' PhyloProfile:::addFeatureColors(seedDf, orthoDf)
addFeatureColors <- function(
seedDf = NULL, orthoDf = NULL, colorType = "all",
colorPalette = "Paired", ignoreInstanceNo = FALSE
) {
if (is.null(seedDf) | is.null(orthoDf)) stop("Domain Df cannot be null!")
feature <- NULL
featureSeedCount <- seedDf %>% dplyr::count(feature)
featureOrthoCount <- orthoDf %>% dplyr::count(feature)
featureCount <- merge(
featureSeedCount, featureOrthoCount, by = "feature", all = TRUE
)
featureCount$type <- "unique"
featureCount$type[featureCount$n.x == featureCount$n.y] <- "shared"
if (ignoreInstanceNo == TRUE) {
featureCount$type[
!is.na(featureCount$n.x) & !is.na(featureCount$n.y)] <- "shared"
}
featureCount$feature <- as.character(featureCount$feature)
sharedFeatures <-unique(featureCount$feature[featureCount$type == "shared"])
uniqueFeatures <-unique(featureCount$feature[featureCount$type == "unique"])
allFeatures <- c(sharedFeatures, uniqueFeatures)
if (colorType == "Unique" & length(uniqueFeatures) == 0)
colorType <- "All"
if (colorType == "Shared" & length(sharedFeatures) == 0)
colorType <- "All"
if (colorType == "Unique") {
sharedFeaturesColors <- rep("#C9C9C9", length(sharedFeatures))
uniqueFeaturesColors <- getQualColForVector(uniqueFeatures)
if (checkColorPalette(uniqueFeatures, colorPalette) == TRUE) {
uniqueFeaturesColors <-
suppressWarnings(head(
RColorBrewer::brewer.pal(
length(uniqueFeatures), colorPalette),
length(uniqueFeatures)
))
}
allColors <- c(sharedFeaturesColors, uniqueFeaturesColors)
colorScheme <- data.frame(color = allColors, feature = allFeatures)
} else if (colorType == "Shared") {
sharedFeaturesColors <- getQualColForVector(sharedFeatures)
uniqueFeaturesColors <- rep("#C9C9C9", length(uniqueFeatures))
if (checkColorPalette(sharedFeatures, colorPalette) == TRUE) {
sharedFeaturesColors <-
suppressWarnings(head(
RColorBrewer::brewer.pal(
length(sharedFeatures), colorPalette),
length(sharedFeatures)
))
}
allColors <- c(sharedFeaturesColors, uniqueFeaturesColors)
colorScheme <- data.frame(color = allColors, feature = allFeatures)
} else if (colorType == "All") {
allColors <- getQualColForVector(allFeatures)
if (checkColorPalette(allFeatures, colorPalette) == TRUE) {
allColors <-
suppressWarnings(head(
RColorBrewer::brewer.pal(length(allFeatures), colorPalette),
length(allFeatures)
))
}
colorScheme <- data.frame(color = allColors, feature = allFeatures)
} else {
tmpDf <- data.frame(str_split_fixed(allFeatures, "_", 2))
tmpDf$name <- paste(tmpDf$X1, tmpDf$X2, sep = "_")
tmpDf$name[tmpDf$X2 == ""] <- tmpDf$X1[tmpDf$X2 == ""]
tmpDf$X2[tmpDf$X2 == ""] <- tmpDf$X1[tmpDf$X2 == ""]
typeColorDf <- data.frame(
colors = head(
suppressWarnings(RColorBrewer::brewer.pal(
nlevels(as.factor(tmpDf$X1)), colorPalette)),
nlevels(as.factor(tmpDf$X1))
),
X1 = levels(as.factor(tmpDf$X1))
)
tmpDf <- merge(tmpDf, typeColorDf, all.x = TRUE)
colorScheme <- data.frame(color = tmpDf$colors, feature = tmpDf$name)
}
# add color to seedDf and orthoDf
seedDf <- merge(seedDf, colorScheme, by = "feature", all.x = TRUE)
orthoDf <- merge(orthoDf, colorScheme, by = "feature", all.x = TRUE)
return(list(seedDf, orthoDf))
}
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