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Refactored function names in R/plotting.R #63

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merged 4 commits into from
Oct 8, 2024
Merged

Refactored function names in R/plotting.R #63

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be3966d
refactored function names in R/plotting.R
teddyCodex Oct 7, 2024
3804b99
update NAMESPACE with roxygen2
teddyCodex Oct 7, 2024
e189cde
Merge commit '3d8ec756487555e7cf64bd716f94937064709f48'
the-mayer Oct 8, 2024
331b651
namespace conflict resolution for other PRs
the-mayer Oct 8, 2024
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22 changes: 11 additions & 11 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,6 @@ export(DownloadAssemblySummary)
export(GCA2lin)
export(GenContextNetwork)
export(IPG2Lineage)
export(LineagePlot)
export(RepresentativeAccNums)
export(acc2FA)
export(acc2Lineage)
Expand Down Expand Up @@ -37,6 +36,8 @@ export(convert_fa2tre)
export(count_bycol)
export(count_to_sunburst)
export(count_to_treemap)
export(createWordCloud2Element)
export(createWordCloudElement)
export(create_all_col_params)
export(create_lineage_lookup)
export(create_one_col_params)
Expand All @@ -60,17 +61,20 @@ export(get_proc_medians)
export(get_proc_weights)
export(ipr2viz)
export(ipr2viz_web)
export(lineage.DA.plot)
export(lineage.Query.plot)
export(lineage.domain_repeats.plot)
export(lineage.neighbors.plot)
export(lineage_sunburst)
export(make_job_results_url)
export(make_opts2procs)
export(mapAcc2Name)
export(map_acc2name)
export(map_advanced_opts2procs)
export(msa_pdf)
export(plotLineageDA)
export(plotLineageDomainRepeats)
export(plotLineageHeatmap)
export(plotLineageNeighbors)
export(plotLineageQuery)
export(plotLineageSunburst)
export(plotStackedLineage)
export(plotUpSet)
export(plot_estimated_walltimes)
export(prot2tax)
export(prot2tax_old)
Expand All @@ -86,9 +90,8 @@ export(run_deltablast)
export(run_rpsblast)
export(selectLongestDuplicate)
export(send_job_status_email)
export(shorten_lineage)
export(shortenLineage)
export(sinkReset)
export(stacked_lin_plot)
export(summ.DA)
export(summ.DA.byLin)
export(summ.GC)
Expand All @@ -98,10 +101,7 @@ export(summarize_bylin)
export(theme_genes2)
export(to_titlecase)
export(total_counts)
export(upset.plot)
export(wordcloud2_element)
export(wordcloud3)
export(wordcloud_element)
export(write.MsaAAMultipleAlignment)
export(write_proc_medians_table)
export(write_proc_medians_yml)
Expand Down
64 changes: 32 additions & 32 deletions R/plotting.R
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Original file line number Diff line number Diff line change
Expand Up @@ -31,9 +31,9 @@
#'
#' @examples
#' \dontrun{
#' shorten_lineage()
#' shortenLineage()
#' }
shorten_lineage <- function(data, colname = "Lineage", abr_len = 1) {
shortenLineage <- function(data, colname = "Lineage", abr_len = 1) {
abbrv <- function(x) {
pos_gt <- str_locate(x, ">")
pos_gt <- pos_gt[1]
Expand Down Expand Up @@ -94,9 +94,9 @@ shorten_lineage <- function(data, colname = "Lineage", abr_len = 1) {
#'
#' @examples
#' \dontrun{
#' upset.plot(pspa.sub, 10, "da2doms")
#' plotUpSet(pspa.sub, 10, "da2doms")
#' }
upset.plot <- function(query_data = "toast_rack.sub",
plotUpSet <- function(query_data = "toast_rack.sub",
colname = "DomArch", cutoff = 90,
RowsCutoff = FALSE, text.scale = 1.5,
point.size = 2.2, line.size = 0.8) {
Expand Down Expand Up @@ -259,9 +259,9 @@ upset.plot <- function(query_data = "toast_rack.sub",
#'
#' @examples
#' \dontrun{
#' lineage.DA.plot(toast_rack_data, 10, "DomArch.norep", "da2doms")
#' plotLineageDA(toast_rack_data, 10, "DomArch.norep", "da2doms")
#' }
lineage.DA.plot <- function(query_data = "prot",
plotLineageDA <- function(query_data = "prot",
colname = "DomArch",
cutoff = 90,
RowsCutoff = FALSE,
Expand All @@ -271,7 +271,7 @@ lineage.DA.plot <- function(query_data = "prot",
# @param type Character. Default is "da2doms" for Domain Architectures.
# Other alternative: "gc2da" for Genomic Contexts. -- unused parameter

query_data <- shorten_lineage(query_data, "Lineage", abr_len = 1)
query_data <- shortenLineage(query_data, "Lineage", abr_len = 1)

query.summ.byLin <- query_data %>% total_counts(cutoff = cutoff, column = colname, RowsCutoff = RowsCutoff)

Expand Down Expand Up @@ -355,9 +355,9 @@ lineage.DA.plot <- function(query_data = "prot",
#'
#' @examples
#' \dontrun{
#' lineage.Query.plot(prot, c("PspA", "PspB", "PspC", "PspM", "PspN"), 95)
#' plotLineageQuery(prot, c("PspA", "PspB", "PspC", "PspM", "PspN"), 95)
#' }
lineage.Query.plot <- function(query_data = all,
plotLineageQuery <- function(query_data = all,
queries,
colname = "ClustName",
cutoff, color = "default") {
Expand Down Expand Up @@ -394,7 +394,7 @@ lineage.Query.plot <- function(query_data = all,
# query_data contains all rows that possess a lineage
query_data <- query_data %>% filter(grepl("a", Lineage))

query_data <- shorten_lineage(query_data, "Lineage", abr_len = 1)
query_data <- shortenLineage(query_data, "Lineage", abr_len = 1)
query_lin_counts <- data.frame("Query" = character(0), "Lineage" = character(0), "count" = integer())
for (q in queries) {
query_lin <- query_by_lineage(data = query_data, query = q, column = {{ col }}, by = "Lineage")
Expand Down Expand Up @@ -492,10 +492,10 @@ lineage.Query.plot <- function(query_data = all,
#'
#' @examples
#' \dontrun{
#' lineage.neighbors.plot(pspa_data, pspa, "GenContext.norep", "da2doms")
#' plotLineageNeighbors(pspa_data, pspa, "GenContext.norep", "da2doms")
#' }
#'
lineage.neighbors.plot <- function(query_data = "prot", query = "pspa",
plotLineageNeighbors <- function(query_data = "prot", query = "pspa",
colname = "GenContext.norep") {
query_data <- query_data %>% filter(grepl("a", Lineage))
query.GCDA <- read_delim(paste0("Top-", query, "-neighbors.txt"),
Expand Down Expand Up @@ -567,9 +567,9 @@ lineage.neighbors.plot <- function(query_data = "prot", query = "pspa",
#'
#' @examples
#' \dontrun{
#' lineage.domain_repeats.plot()
#' plotLineageDomainRepeats()
#' }
lineage.domain_repeats.plot <- function(query_data, colname) {
plotLineageDomainRepeats <- function(query_data, colname) {
# query_data <- pspa_data
# colname <- "SIG.TM.LADB"

Expand Down Expand Up @@ -629,7 +629,7 @@ lineage.domain_repeats.plot <- function(query_data, colname) {
}


#' LineagePlot
#' plotLineageHeatmap
#'
#' @description
#' Generate a lineage plot
Expand All @@ -651,7 +651,7 @@ lineage.domain_repeats.plot <- function(query_data, colname) {
#'
#' @examples
#' \dontrun{
#' LineagePlot(psp_data,
#' plotLineageHeatmap(psp_data,
#' c(
#' "PspA", "Snf7", "Classical-AAA", "PspF", "PspB", "PspC", "ClgR", "PspM",
#' "Thioredoxin", "PspN_N", "DUF3046", "LiaI-LiaF-TM", "Toast_rack", "REC",
Expand All @@ -664,8 +664,8 @@ lineage.domain_repeats.plot <- function(query_data, colname) {
#' )
#' }
#'
LineagePlot <- function(prot, domains_of_interest, level = 3, label.size = 8) {
LevelReduction <- function(lin) {
plotLineageHeatmap <- function(prot, domains_of_interest, level = 3, label.size = 8) {
.LevelReduction <- function(lin) {
if (level == 1) {
gt_loc <- str_locate(lin, ">")[[1]]
if (is.na(gt_loc)) {
Expand Down Expand Up @@ -703,7 +703,7 @@ LineagePlot <- function(prot, domains_of_interest, level = 3, label.size = 8) {
all_grouped <- dplyr::union(all_grouped, domSub)
}

GetKingdom <- function(lin) {
.GetKingdom <- function(lin) {
gt_loc <- str_locate(lin, ">")[, "start"]

if (is.na(gt_loc)) {
Expand All @@ -715,12 +715,12 @@ LineagePlot <- function(prot, domains_of_interest, level = 3, label.size = 8) {
}
}

all_grouped <- all_grouped %>% mutate(ReducedLin = unlist(purrr::map(Lineage, LevelReduction)))
all_grouped <- all_grouped %>% mutate(ReducedLin = unlist(purrr::map(Lineage, .LevelReduction)))

all_grouped_reduced <- all_grouped %>%
group_by(Query, ReducedLin) %>%
summarize("count" = sum(count)) %>%
mutate(Kingdom = unlist(purrr::map(ReducedLin, GetKingdom)))
mutate(Kingdom = unlist(purrr::map(ReducedLin, .GetKingdom)))

lin_counts <- all_grouped_reduced %>%
group_by(Kingdom, ReducedLin) %>%
Expand Down Expand Up @@ -814,9 +814,9 @@ LineagePlot <- function(prot, domains_of_interest, level = 3, label.size = 8) {
#'
#' @examples
#' \dontrun{
#' stacked_lin_plot()
#' plotStackedLineage()
#' }
stacked_lin_plot <- function(prot, column = "DomArch", cutoff, Lineage_col = "Lineage",
plotStackedLineage <- function(prot, column = "DomArch", cutoff, Lineage_col = "Lineage",
xlabel = "Domain Architecture",
reduce_lineage = TRUE,
label.size = 8,
Expand All @@ -828,7 +828,7 @@ stacked_lin_plot <- function(prot, column = "DomArch", cutoff, Lineage_col = "Li
col <- sym(column)

if (reduce_lineage) {
prot <- shorten_lineage(prot, Lineage_col, abr_len = 3)
prot <- shortenLineage(prot, Lineage_col, abr_len = 3)
}

total_count <- total_counts(prot, column, cutoff, lineage_col = Lineage_col)
Expand Down Expand Up @@ -935,7 +935,7 @@ stacked_lin_plot <- function(prot, column = "DomArch", cutoff, Lineage_col = "Li
################
#### NEEDS SOME WORK

#' Wordcloud3
#' plotWordCloud3
#'
#' @param data
#' @param size
Expand Down Expand Up @@ -1048,9 +1048,9 @@ wordcloud3 <- function(data, size = 1, minSize = 0, gridSize = 0, fontFamily = "
#'
#' @examples
#' \dontrun{
#' wordcloud_element(prot, "da2doms", 10)
#' createWordCloudElement(prot, "da2doms", 10)
#' }
wordcloud_element <- function(query_data = "prot",
createWordCloudElement <- function(query_data = "prot",
colname = "DomArch",
cutoff = 70,
UsingRowsCutoff = FALSE) {
Expand Down Expand Up @@ -1125,9 +1125,9 @@ wordcloud_element <- function(query_data = "prot",
#'
#' @examples
#' \dontrun{
#' wordcloud_element(prot, "da2doms", 10)
#' createWordCloudElement(prot, "da2doms", 10)
#' }
wordcloud2_element <- function(query_data = "prot",
createWordCloud2Element <- function(query_data = "prot",
colname = "DomArch",
cutoff = 70,
UsingRowsCutoff = FALSE) {
Expand Down Expand Up @@ -1194,9 +1194,9 @@ wordcloud2_element <- function(query_data = "prot",
#'
#' @examples
#' \dontrun{
#' lineage_sunburst()
#' plotLineageSunburst()
#' }
lineage_sunburst <- function(prot, lineage_column = "Lineage",
plotLineageSunburst <- function(prot, lineage_column = "Lineage",
type = "sunburst",
levels = 2, colors = NULL, legendOrder = NULL, showLegend = TRUE, maxLevels = 5) {
lin_col <- sym(lineage_column)
Expand Down Expand Up @@ -1278,7 +1278,7 @@ lineage_sunburst <- function(prot, lineage_column = "Lineage",


## COMMENTED LINEAGE.DA.PLOT
# lineage.plot <- function(query_data, cutoff, type) {
# plotLineage <- function(query_data, cutoff, type) {
# switch(type,
# da2doms={wc <- DA.doms.wc; words <- toast_rack.DAdoms; colname <- "DomArch.norep"; toast_rack.summ.byLin <- toast_rack.DA.summ.byLin}, # elements <- toast_rack.DA;
# gc2da={wc <- GC.DA.wc; words <- toast_rack.GCDA; colname <- "GenContext.norep"; toast_rack.summ.byLin <- toast_rack.GC.summ.byLin} # elements <- toast_rack.GC;
Expand Down
8 changes: 4 additions & 4 deletions man/wordcloud2_element.Rd → man/createWordCloud2Element.Rd
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8 changes: 4 additions & 4 deletions man/wordcloud_element.Rd → man/createWordCloudElement.Rd
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8 changes: 4 additions & 4 deletions man/lineage.DA.plot.Rd → man/plotLineageDA.Rd
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8 changes: 4 additions & 4 deletions man/lineage.domain_repeats.plot.Rd → man/plotLineageDomainRepeats.Rd
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10 changes: 5 additions & 5 deletions man/LineagePlot.Rd → man/plotLineageHeatmap.Rd
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