Nothing
R/openxlsxCommands.R
In vanddraabe: Identification and Statistical Analysis of Conserved Waters Near Proteins
## openxlsxCommands.R :: the molecular similarity within a dataset
##
## NOTE!!!! THESE FUNCTIONS ARE HIGHLY SPECIFIC AND ARE MEANT TO BE USED WITH
## THE INDICATED FUNCTION(S) AND data.frames.
##
## apr-15-2016 (exe) created
## apr-25-2016 (exe) added the AlignOverlap worksheet
## apr-25-2016 (exe) updated documentation
## feb-09-2017 (exe) updated documentation (rMarkdown)
## mar-15-2017 (exe) updated documentation (rMarkdown)
## apr-14-2017 (exe) added the Cleaned PDB Summary worksheet for
## CleanProteinStructures()
## apr-14-2017 (exe) added oxPlainDataSheet() to construct a plain worksheet
## jul-25-2017 (exe) updated documentation
## jul-31-2017 (exe) updated oxPDBcleanedSummarySheet() and oxPlainDataSheet()
## documentation
## jul-31-2017 (exe) updated documentation to indicate cell formatting
## aug-02-2017 (exe) updated documentation
## aug-07-2017 (exe) added cell formatting for "*.calc" to oxClusterSummarySheet()
##
## Please direct all questions to Emilio Xavier Esposito, PhD
## exeResearch LLC, East Lansing, Michigan 48823 USA
## http://www.exeResearch.com
## emilio AT exeResearch DOT com
## emilio DOT esposito AT gmail DOT com
##
## Copyright (c) 2017, Emilio Xavier Esposito
##
## Permission is hereby granted, free of charge, to any person obtaining
## a copy of this software and associated documentation files (the
## "Software"), to deal in the Software without restriction, including
## without limitation the rights to use, copy, modify, merge, publish,
## distribute, sublicense, and/or sell copies of the Software, and to
## permit persons to whom the Software is furnished to do so, subject to
## the following conditions:
##
## The above copyright notice and this permission notice shall be
## included in all copies or substantial portions of the Software.
##
## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
## EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
## MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
## NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
## LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
## OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
## WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
##
## Based on http://opensource.org/licenses/MIT
##
## oxClusterStatsSheet docs ---------------------------------------------------------
#' @title openxlsx Water Cluster Statistics
#' @description Constructs the [openxlsx] worksheet for the Water
#' Cluster statistics.
#' @details **This function is to _ONLY_ be used with the results of
#' [ConservedWaterStats()]**. Specific aspects of how the
#' returned `data.frame` will be formatted are **hard-coded** into this
#' function.
#'
#' This [openxlsx] function is _**NOT**_ exported.
#'
#' @param wb.name Name of the workbook for the results; _e.g._, results.wb
#' @param sheet.name Name of the worksheet being formatted; default:
#' "ClusterStatistics"
#' @param df data.frame containing the results of the `GetSimilarityPairs`
#' function; _e.g._, `h2o.cluster.stats`
#'
#' @return The workbook containing the indicated and newly formatted worksheet.
#'
#' @import openxlsx
#'
#' @author Emilio Xavier Esposito \email{emilio@@exeResearch.com}
#'
#' @family "openxlsx functions"
#'
oxClusterStatsSheet <- function(wb.name,
sheet.name = "ClusterStatistics",
df) {
##----- add sheet
openxlsx::addWorksheet(wb = wb.name, sheetName = sheet.name, gridLines = TRUE)
##----- add data
openxlsx::writeData(wb = wb.name,
sheet = sheet.name,
x = df,
startCol = 1,
startRow = 3,
colNames = FALSE,
rowNames = TRUE,
keepNA = FALSE,
withFilter = FALSE,
headerStyle = NULL)
##----- merge cells for titles
openxlsx::mergeCells(wb = wb.name,
sheet = sheet.name,
cols = 2:3,
rows = 1)
openxlsx::mergeCells(wb = wb.name,
sheet = sheet.name,
cols = 4:5,
rows = 1)
##----- add table titles
openxlsx::writeData(wb = wb.name,
sheet = sheet.name,
startCol = 2,
startRow = 1,
x = "All Waters")
openxlsx::writeData(wb = wb.name,
sheet = sheet.name,
startCol = 4,
startRow = 1,
x = "Passed Waters")
openxlsx::writeData(wb = wb.name,
sheet = sheet.name,
startCol = 2,
startRow = 2,
x = "Number")
openxlsx::writeData(wb = wb.name,
sheet = sheet.name,
startCol = 3,
startRow = 2,
x = "Percentage (%)")
openxlsx::writeData(wb = wb.name,
sheet = sheet.name,
startCol = 4,
startRow = 2,
x = "Number")
openxlsx::writeData(wb = wb.name,
sheet = sheet.name,
startCol = 5,
startRow = 2,
x = "Percentage (%)")
##----- set column widths
openxlsx::setColWidths(wb = wb.name,
sheet = sheet.name,
cols = 1:5,
widths = "auto")
##----- number of digits for "Average conservation"
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.2digits,
cols = c(2, 4),
rows = 7,
gridExpand = TRUE,
stack = TRUE)
##----- number of digits for percentage of clusters with various proportions
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.titles.tables,
cols = c(2:5),
rows = c(1:2),
gridExpand = TRUE,
stack = TRUE)
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.1digits,
cols = c(3, 5),
rows = c(8:13),
gridExpand = TRUE,
stack = TRUE)
##----- number of digits for calculation times
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.comma,
cols = c(2, 4),
rows = c(3:6,14),
gridExpand = TRUE,
stack = TRUE)
##----- number of digits for calculation times
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.4digits,
cols = c(2, 4),
rows = c(16:17),
gridExpand = TRUE,
stack = TRUE)
##----- return the workbook
return(wb.name)
}
## oxWaterOccurrenceSheet docs -------------------------------------------------------
#' @title openxlsx Water Occurrence Summary
#' @description Constructs the [openxlsx] worksheet for the Water Occurrence
#' summary.
#' @details **This function is to _ONLY_ be used with the results of
#' [ConservedWaters()]**. Specific aspects of how the
#' returned `data.frame` will be formatted are **hard-coded** into this
#' function.
#'
#' This [openxlsx] function is _**NOT**_ exported.
#'
#' @param wb.name Name of the workbook for the results; _e.g._, results.wb
#' @param sheet.name Name of the worksheet being formatted; default:
#' `"WaterOccurrenceSummary"`
#' @param df data.frame containing the water occurrence results of the
#' [ConservedWaters()] function; _e.g._, `h2o.occurrence`
#'
#' @return The workbook containing the indicated and newly formatted worksheet.
#'
#' @import openxlsx
#'
#' @author Emilio Xavier Esposito \email{emilio@@exeResearch.com}
#'
#' @family "openxlsx functions"
#'
oxWaterOccurrenceSheet <- function(wb.name,
sheet.name = "WaterOccurrenceSummary",
df) {
##----- data.frame dimensions and other information
df.size <- dim(df)
df.row.idc <- 2:(df.size[1] + 1)
df.col.idc <- 1:(df.size[2] + 1)
df.colnames <- colnames(df)
##----- add sheet
openxlsx::addWorksheet(wb = wb.name,
sheetName = sheet.name,
gridLines = TRUE)
##----- add data
openxlsx::writeDataTable(wb = wb.name,
sheet = sheet.name,
x = as.data.frame(df, stringsAsFactors = FALSE),
colNames = TRUE,
rowNames = TRUE,
tableStyle = "none",
withFilter = FALSE,
headerStyle = cs.header)
##----- freeze the panes
openxlsx::freezePane(wb = wb.name,
sheet = sheet.name,
firstRow = TRUE, firstCol = TRUE)
##----- set column widths
openxlsx::setColWidths(wb = wb.name,
sheet = sheet.name,
cols = df.col.idc,
widths = "auto")
##----- number of digits
##--- the resolution column
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.2digits,
cols = 2,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- the rObserved and rFree columns
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.3digits,
cols = c(3, 4),
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- the means columns
mu.cols.idc <- grep(pattern = ".mu", df.colnames) + 1
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.2digits,
cols = mu.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- the standard deviation columns
sd.cols.idc <- grep(pattern = ".sd", df.colnames) + 1
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.3digits,
cols = sd.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- the percent
pct.cols.idc <- grep(pattern = "pct.", df.colnames) + 1
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.1digits,
cols = pct.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##----- color-code the cluster true-false table
cluster.cols.idc <- grep(pattern = "clust_", df.colnames) + 1
openxlsx::conditionalFormatting(wb = wb.name,
sheet = sheet.name,
cols = cluster.cols.idc,
rows = df.row.idc,
type = "contains",
rule = "TRUE",
style = cs.green)
openxlsx::conditionalFormatting(wb = wb.name,
sheet = sheet.name,
cols = cluster.cols.idc,
rows = df.row.idc,
type = "contains",
rule = "FALSE",
style = cs.pink)
##----- return the workbook
return(wb.name)
}
## oxClusterSummarySheet docs --------------------------------------------------
#' @title openxlsx Cluster Summary Sheet
#' @description Constructs the [openxlsx] worksheet for the Cluster Summary
#' analysis.
#' @details **This function is to _ONLY_ be used with the results of
#' [ConservedWaters()]**. Specific aspects of how the
#' returned `data.frame` will be formatted are **hard-coded** into this
#' function.
#'
#' This [openxlsx] function is _**NOT**_ exported.
#'
#' @param wb.name Name of the workbook for the results; _e.g._, results.wb
#' @param sheet.name Name of the worksheet being formatted; default:
#' `"ClusterSummary"`
#' @param df data.frame containing the cluster summary from the
#' [ConservedWaters()] function; _e.g._, `h2o.clusters.summary`
#'
#' @return The workbook containing the indicated and newly formatted worksheet.
#'
#' @import openxlsx
#'
#' @author Emilio Xavier Esposito \email{emilio@@exeResearch.com}
#'
#' @family "openxlsx functions"
#'
oxClusterSummarySheet <- function(wb.name,
sheet.name = "ClusterSummary",
df) {
##----- data.frame dimensions and other information
df.size <- dim(df)
df.row.idc <- 2:(df.size[1] + 1)
df.col.idc <- 1:df.size[2]
df.colnames <- colnames(df)
##----- add sheet
openxlsx::addWorksheet(wb = wb.name,
sheetName = sheet.name,
gridLines = TRUE)
##----- add data
openxlsx::writeDataTable(wb = wb.name,
sheet = sheet.name,
x = as.data.frame(df, stringsAsFactors = FALSE),
colNames = TRUE,
rowNames = FALSE,
tableStyle = "none",
withFilter = FALSE,
headerStyle = cs.header)
##----- freeze the panes
openxlsx::freezePane(wb = wb.name,
sheet = sheet.name,
firstRow = FALSE, firstActiveRow = 2,
firstCol = FALSE, firstActiveCol = 4)
##----- set column widths
openxlsx::setColWidths(wb = wb.name,
sheet = sheet.name,
cols = df.col.idc,
widths = "auto")
##----- number of digits
##--- the x, y, and z columns
xyz.cols.idc <- which(df.colnames %in% c("x", "y", "z"))
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.3digits,
cols = xyz.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- the calc columns
mu.cols.idc <- grep(pattern = ".calc", df.colnames)
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.2digits,
cols = mu.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- the means columns
mu.cols.idc <- grep(pattern = ".mu", df.colnames)
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.2digits,
cols = mu.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- the standard deviation columns
sd.cols.idc <- grep(pattern = ".sd", df.colnames)
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.3digits,
cols = sd.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- the percent
pct.cols.idc <- grep(pattern = "pct.", df.colnames)
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.1digits,
cols = pct.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- the rmsf column
rmsf.cols.idc <- grep(pattern = "rmsf", df.colnames)
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.4digits,
cols = rmsf.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- the means columns
mobility.cols.idc <- grep(pattern = "mobility", df.colnames)
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.2digits,
cols = mobility.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##----- return the workbook
return(wb.name)
}
## oxRCSBinfoSheet docs --------------------------------------------------
#' @title openxlsx PDB/RCSB Summary Sheet
#' @description Constructs the [openxlsx] worksheet for the Similarity
#' Summary analysis.
#' @details **This function is to _ONLY_ be used with the results of
#' [ConservedWaters()]**. Specific aspects of how the
#' returned `data.frame` will be formatted are **hard-coded** into this
#' function.
#'
#' This [openxlsx] function is _**NOT**_ exported.
#'
#' @param wb.name Name of the workbook for the results; _e.g._, results.wb
#' @param sheet.name Name of the worksheet being formatted; default:
#' "PDB_information"
#' @param df data.frame containing the PDB/RCSB information obtatined within the
#' [ConservedWaters()] function; _e.g._, `pdbs.information`
#'
#' @return The workbook containing the indicated and newly formatted worksheet.
#'
#' @import openxlsx
#'
#' @author Emilio Xavier Esposito \email{emilio@@exeResearch.com}
#'
#' @family "openxlsx functions"
#'
oxRCSBinfoSheet <- function(wb.name,
sheet.name = "RCSB_information",
df) {
##----- data.frame dimensions and other information
df.size <- dim(df)
df.row.idc <- 2:(df.size[1] + 1)
df.col.idc <- 1:df.size[2]
df.colnames <- colnames(df)
##----- add sheet
openxlsx::addWorksheet(wb = wb.name,
sheetName = sheet.name,
gridLines = TRUE)
##----- add data
openxlsx::writeDataTable(wb = wb.name,
sheet = sheet.name,
x = as.data.frame(df, stringsAsFactors = FALSE),
colNames = TRUE,
rowNames = FALSE,
tableStyle = "none",
withFilter = FALSE,
headerStyle = cs.header)
##----- freeze the panes
openxlsx::freezePane(wb = wb.name,
sheet = sheet.name,
firstRow = FALSE, firstActiveRow = 2,
firstCol = FALSE, firstActiveCol = 5)
##----- set column widths
openxlsx::setColWidths(wb = wb.name,
sheet = sheet.name,
cols = df.col.idc,
widths = "auto")
##----- set the date format
depositionDate.idx <- which(df.colnames == "depositionDate")
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.date,
cols = depositionDate.idx,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##----- return the workbook
return(wb.name)
}
## oxInitWaterDataSheet docs ---------------------------------------------------
#' @title Initial Water Data Sheet
#' @description Constructs the [openxlsx] worksheet for the initial water data.
#' @details **This function is to _ONLY_ be used with the results of
#' [ConservedWaters()]**. Specific aspects of how the
#' returned `data.frame` will be formatted are **hard-coded** into this
#' function.
#'
#' This [openxlsx] function is _**NOT**_ exported.
#'
#' @param wb.name Name of the workbook for the results; _e.g._, results.wb
#' @param sheet.name Name of the worksheet being formatted; default:
#' `"InitialWaterData"`
#' @param df data.frame containing the concatenate initial waters with
#' experimental and experimentally derived values obtatined within the
#' [ConservedWaters()] function; _e.g._, `h2o.df`
#'
#' @return The workbook containing the indicated and newly formatted worksheet.
#'
#' @import openxlsx
#'
#' @author Emilio Xavier Esposito \email{emilio@@exeResearch.com}
#'
#' @family "openxlsx functions"
#'
oxInitWaterDataSheet <- function(wb.name,
sheet.name = "InitialWaterData",
df) {
##_ data.frame dimensions and other information -----
df.size <- dim(df)
df.row.idc <- 2:(df.size[1] + 1)
df.col.idc <- 1:(df.size[2] + 1)
df.colnames <- colnames(df)
##_ add sheet -----
openxlsx::addWorksheet(wb = wb.name,
sheetName = sheet.name,
gridLines = TRUE)
##_ add data -----
openxlsx::writeDataTable(wb = wb.name,
sheet = sheet.name,
x = as.data.frame(df, stringsAsFactors = FALSE),
colNames = TRUE,
rowNames = TRUE,
tableStyle = "none",
withFilter = FALSE,
headerStyle = cs.header)
##_ freeze the panes -----
openxlsx::freezePane(wb = wb.name, sheet = sheet.name,
firstRow = TRUE, firstCol = TRUE)
##_ set column widths -----
openxlsx::setColWidths(wb = wb.name, sheet = sheet.name,
cols = df.col.idc, widths = "auto")
##_ number of digits -----
##--- the x, y, and z columns
xyz.cols.idc <- which(df.colnames %in% c("x", "y", "z")) + 1
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.3digits,
cols = xyz.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- atom number column
eleno.cols.idc <- which(df.colnames %in% c("eleno")) + 1
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.0digits,
cols = eleno.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- occupation, B-value, mobility, and normalized B-values column
ob.cols.idc <- which(df.colnames %in% c("o","b","mobility","nBvalue")) + 1
openxlsx::addStyle(wb = wb.name, sheet = sheet.name, style = cs.2digits,
cols = ob.cols.idc, rows = df.row.idc,
gridExpand = TRUE, stack = TRUE)
##--- the resolution column
res.col.idc <- grep(pattern = "resolution", df.colnames) + 1
openxlsx::addStyle(wb = wb.name, sheet = sheet.name, style = cs.2digits,
cols = res.col.idc, rows = df.row.idc,
gridExpand = TRUE, stack = TRUE)
##--- the rObserved and rFree columns
res.col.idc <- c(grep(pattern = "rObserved", df.colnames),
grep(pattern = "rFree", df.colnames) ) + 1
openxlsx::addStyle(wb = wb.name, sheet = sheet.name, style = cs.3digits,
cols = c(3, 4), rows = df.row.idc,
gridExpand = TRUE, stack = TRUE)
##--- the summation columns
sum.cols.idc <- grep(pattern = ".sum", df.colnames) + 1
openxlsx::addStyle(wb = wb.name, sheet = sheet.name, style = cs.3digits,
cols = sum.cols.idc, rows = df.row.idc,
gridExpand = TRUE, stack = TRUE)
##--- the means columns
mu.cols.idc <- grep(pattern = ".mu", df.colnames) + 1
openxlsx::addStyle(wb = wb.name, sheet = sheet.name, style = cs.2digits,
cols = mu.cols.idc, rows = df.row.idc,
gridExpand = TRUE, stack = TRUE)
##--- the standard deviation columns
sd.cols.idc <- grep(pattern = ".sd", df.colnames) + 1
openxlsx::addStyle(wb = wb.name, sheet = sheet.name, style = cs.3digits,
cols = sd.cols.idc, rows = df.row.idc,
gridExpand = TRUE, stack = TRUE)
##_ color-code the cluster true-false table -----
tf.cols.idc <- c(grep(pattern = ".keep", df.colnames),
grep(pattern = ".cutoffs", df.colnames) ) + 1
openxlsx::conditionalFormatting(wb = wb.name, sheet = sheet.name,
cols = tf.cols.idc, rows = df.row.idc,
type = "contains", rule = "TRUE",
style = cs.green)
openxlsx::conditionalFormatting(wb = wb.name, sheet = sheet.name,
cols = tf.cols.idc, rows = df.row.idc,
type = "contains", rule = "FALSE",
style = cs.pink)
##_ return the workbook -----
return(wb.name)
}
## oxAlignOverlapSheet docs ----------------------------------------------------
#' @title Align Overlap Data Sheet
#' @description Constructs the [openxlsx] worksheet for the
#' [AlignOverlap()] results.
#' @details **This function is to _ONLY_ be used with the results of
#' [AlignOverlap()]**. Specific aspects of how the
#' returned `data.frame` will be formatted are **hard-coded** into this
#' function.
#'
#' Notable formatting:
#' - Top row frozen
#' - Column widths are set based on column content
#' - Structures passing the [AlignOverlap()] evaluation are hightlighted
#' lime green
#' - Structures failing the [AlignOverlap()] evaluation are hightlighted
#' pink
#'
#' This [openxlsx] function is _**NOT**_ exported.
#'
#' @param wb.name Name of the workbook for the results; _e.g._, results.wb
#' @param sheet.name Name of the worksheet being formatted; default:
#' `"AlignOverlap"`
#' @param df data.frame containing the summary of [AlignOverlap()]; _e.g._,
#' `df.results`
#'
#' @return The workbook containing the indicated and newly formatted worksheet.
#'
#' @import openxlsx
#'
#' @author Emilio Xavier Esposito \email{emilio@@exeResearch.com}
#'
#' @family "openxlsx functions"
#'
oxAlignOverlapSheet <- function(wb.name,
sheet.name = "AlignOverlap",
df) {
##----- data.frame dimensions and other information
df.size <- dim(df)
df.row.idc <- 2:(df.size[1] + 1)
df.col.idc <- 1:(df.size[2] + 1)
df.colnames <- colnames(df)
##----- add sheet
openxlsx::addWorksheet(wb = wb.name,
sheetName = sheet.name,
gridLines = TRUE)
##----- add data
openxlsx::writeDataTable(wb = wb.name,
sheet = sheet.name,
x = as.data.frame(df, stringsAsFactors = FALSE),
colNames = TRUE,
rowNames = FALSE,
tableStyle = "none",
withFilter = FALSE,
headerStyle = cs.header)
##----- freeze the panes
openxlsx::freezePane(wb = wb.name,
sheet = sheet.name,
firstRow = TRUE,
firstCol = FALSE)
##----- set column widths
openxlsx::setColWidths(wb = wb.name,
sheet = sheet.name,
cols = df.col.idc,
widths = "auto")
##----- color-code the cluster true-false table
openxlsx::conditionalFormatting(wb = wb.name,
sheet = sheet.name,
cols = c(2, 5),
rows = df.row.idc,
type = "contains",
rule = "TRUE",
style = cs.green)
openxlsx::conditionalFormatting(wb = wb.name,
sheet = sheet.name,
cols = c(2, 5),
rows = df.row.idc,
type = "contains",
rule = "FALSE",
style = cs.pink)
##----- return the workbook
return(wb.name)
}
## oxPDBcleanedSummarySheet docs -----------------------------------------------
#' @title Cleaned PDB Structures Data Sheet
#' @description Constructs the [openxlsx] worksheet for the
#' [CleanProteinStructures()] results.
#' @details **This function is to _ONLY_ be used with the results of
#' [CleanProteinStructures()]**. Specific aspects of how the
#' returned `data.frame` will be formatted are **hard-coded** into this
#' function.
#'
#' Notable formatting:
#' - Top row frozen
#' - Column widths are set based on column content
#' - Structures with hydrogen atoms removed are highlighted with amber cell color
#' - Structures with OoR values, modeled atoms, and removed waters are highlighted
#' with amber cell color
#'
#' This [openxlsx] function is _**NOT**_ exported.
#'
#' @param wb.name Name of the workbook for the results; _e.g._, results.wb
#' @param sheet.name Name of the worksheet being formatted; default:
#' `"PDBcleanedSummary"`
#' @param df data.frame containing the summary of
#' [CleanProteinStructures()]; _e.g._, `df.results`
#'
#' @return The workbook containing the indicated and newly formatted worksheet.
#'
#' @import openxlsx
#'
#' @author Emilio Xavier Esposito \email{emilio@@exeResearch.com}
#'
#' @family "openxlsx functions"
#'
oxPDBcleanedSummarySheet <- function(wb.name,
sheet.name = "PDBcleanedSummary",
df) {
##----- data.frame dimensions and other information
df.size <- dim(df)
df.row.idc <- 2:(df.size[1] + 1)
df.col.idc <- 1:(df.size[2] + 1)
df.colnames <- colnames(df)
##----- add sheet
openxlsx::addWorksheet(wb = wb.name,
sheetName = sheet.name,
gridLines = TRUE)
##----- add data
openxlsx::writeDataTable(wb = wb.name,
sheet = sheet.name,
x = as.data.frame(df, stringsAsFactors = FALSE),
colNames = TRUE,
rowNames = FALSE,
tableStyle = "none",
withFilter = FALSE,
headerStyle = cs.header)
##----- freeze the panes
openxlsx::freezePane(wb = wb.name,
sheet = sheet.name,
firstRow = TRUE,
firstCol = FALSE)
##----- set column widths
openxlsx::setColWidths(wb = wb.name,
sheet = sheet.name,
cols = df.col.idc,
widths = "auto")
##----- color structures with removed hydrogens amber
openxlsx::conditionalFormatting(wb = wb.name,
sheet = sheet.name,
cols = c(2),
rows = df.row.idc,
type = "contains",
rule = "TRUE",
style = cs.amber)
##----- color values for structures with OoR values, modeled atoms, and
## removed waters
openxlsx::conditionalFormatting(wb = wb.name,
sheet = sheet.name,
cols = c(3, 4, 5),
rows = df.row.idc,
type = "expression",
rule = "!=0",
style = cs.amber)
openxlsx::conditionalFormatting(wb = wb.name,
sheet = sheet.name,
cols = c(7),
rows = df.row.idc,
type = "expression",
rule = "!=0",
style = cs.amber)
##----- return the workbook
return(wb.name)
}
## oxPlainDataSheet docs -------------------------------------------------------
#' @title Plain Data Sheet
#' @description Constructs a plain Excel worksheet via the [openxlsx] package.
#' @details **This function creates a basic Excel worksheet with minimal
#' formatting.**
#'
#' Notable formatting:
#' - Top row frozen
#' - Column widths are set based on column content
#'
#' This [openxlsx] function is _**NOT**_ exported.
#'
#' @param wb.name Name of the workbook for the results; _e.g._, results.wb
#' @param sheet.name Name of the worksheet being formatted; default:
#' `"basic"`
#' @param df data.frame containing the data to be written; _e.g._, `df.results`
#'
#' @return The workbook containing the indicated and newly formatted worksheet.
#'
#' @import openxlsx
#'
#' @author Emilio Xavier Esposito \email{emilio@@exeResearch.com}
#'
#' @family "openxlsx functions"
#'
oxPlainDataSheet <- function(wb.name,
sheet.name = "basic",
df) {
##----- data.frame dimensions and other information
df.size <- dim(df)
df.row.idc <- 2:(df.size[1] + 1)
df.col.idc <- 1:(df.size[2] + 1)
df.colnames <- colnames(df)
##----- add sheet
openxlsx::addWorksheet(wb = wb.name,
sheetName = sheet.name,
gridLines = TRUE)
##----- add data
openxlsx::writeDataTable(wb = wb.name,
sheet = sheet.name,
x = as.data.frame(df, stringsAsFactors = FALSE),
colNames = TRUE,
rowNames = FALSE,
tableStyle = "none",
withFilter = FALSE,
headerStyle = cs.header)
##----- freeze the panes
openxlsx::freezePane(wb = wb.name,
sheet = sheet.name,
firstRow = TRUE,
firstCol = TRUE)
##----- set column widths
openxlsx::setColWidths(wb = wb.name,
sheet = sheet.name,
cols = df.col.idc,
widths = "auto")
##----- return the workbook
return(wb.name)
}
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## openxlsxCommands.R :: the molecular similarity within a dataset
##
## NOTE!!!! THESE FUNCTIONS ARE HIGHLY SPECIFIC AND ARE MEANT TO BE USED WITH
## THE INDICATED FUNCTION(S) AND data.frames.
##
## apr-15-2016 (exe) created
## apr-25-2016 (exe) added the AlignOverlap worksheet
## apr-25-2016 (exe) updated documentation
## feb-09-2017 (exe) updated documentation (rMarkdown)
## mar-15-2017 (exe) updated documentation (rMarkdown)
## apr-14-2017 (exe) added the Cleaned PDB Summary worksheet for
## CleanProteinStructures()
## apr-14-2017 (exe) added oxPlainDataSheet() to construct a plain worksheet
## jul-25-2017 (exe) updated documentation
## jul-31-2017 (exe) updated oxPDBcleanedSummarySheet() and oxPlainDataSheet()
## documentation
## jul-31-2017 (exe) updated documentation to indicate cell formatting
## aug-02-2017 (exe) updated documentation
## aug-07-2017 (exe) added cell formatting for "*.calc" to oxClusterSummarySheet()
##
## Please direct all questions to Emilio Xavier Esposito, PhD
## exeResearch LLC, East Lansing, Michigan 48823 USA
## http://www.exeResearch.com
## emilio AT exeResearch DOT com
## emilio DOT esposito AT gmail DOT com
##
## Copyright (c) 2017, Emilio Xavier Esposito
##
## Permission is hereby granted, free of charge, to any person obtaining
## a copy of this software and associated documentation files (the
## "Software"), to deal in the Software without restriction, including
## without limitation the rights to use, copy, modify, merge, publish,
## distribute, sublicense, and/or sell copies of the Software, and to
## permit persons to whom the Software is furnished to do so, subject to
## the following conditions:
##
## The above copyright notice and this permission notice shall be
## included in all copies or substantial portions of the Software.
##
## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
## EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
## MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
## NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
## LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
## OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
## WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
##
## Based on http://opensource.org/licenses/MIT
##
## oxClusterStatsSheet docs ---------------------------------------------------------
#' @title openxlsx Water Cluster Statistics
#' @description Constructs the [openxlsx] worksheet for the Water
#' Cluster statistics.
#' @details **This function is to _ONLY_ be used with the results of
#' [ConservedWaterStats()]**. Specific aspects of how the
#' returned `data.frame` will be formatted are **hard-coded** into this
#' function.
#'
#' This [openxlsx] function is _**NOT**_ exported.
#'
#' @param wb.name Name of the workbook for the results; _e.g._, results.wb
#' @param sheet.name Name of the worksheet being formatted; default:
#' "ClusterStatistics"
#' @param df data.frame containing the results of the `GetSimilarityPairs`
#' function; _e.g._, `h2o.cluster.stats`
#'
#' @return The workbook containing the indicated and newly formatted worksheet.
#'
#' @import openxlsx
#'
#' @author Emilio Xavier Esposito \email{emilio@@exeResearch.com}
#'
#' @family "openxlsx functions"
#'
oxClusterStatsSheet <- function(wb.name,
sheet.name = "ClusterStatistics",
df) {
##----- add sheet
openxlsx::addWorksheet(wb = wb.name, sheetName = sheet.name, gridLines = TRUE)
##----- add data
openxlsx::writeData(wb = wb.name,
sheet = sheet.name,
x = df,
startCol = 1,
startRow = 3,
colNames = FALSE,
rowNames = TRUE,
keepNA = FALSE,
withFilter = FALSE,
headerStyle = NULL)
##----- merge cells for titles
openxlsx::mergeCells(wb = wb.name,
sheet = sheet.name,
cols = 2:3,
rows = 1)
openxlsx::mergeCells(wb = wb.name,
sheet = sheet.name,
cols = 4:5,
rows = 1)
##----- add table titles
openxlsx::writeData(wb = wb.name,
sheet = sheet.name,
startCol = 2,
startRow = 1,
x = "All Waters")
openxlsx::writeData(wb = wb.name,
sheet = sheet.name,
startCol = 4,
startRow = 1,
x = "Passed Waters")
openxlsx::writeData(wb = wb.name,
sheet = sheet.name,
startCol = 2,
startRow = 2,
x = "Number")
openxlsx::writeData(wb = wb.name,
sheet = sheet.name,
startCol = 3,
startRow = 2,
x = "Percentage (%)")
openxlsx::writeData(wb = wb.name,
sheet = sheet.name,
startCol = 4,
startRow = 2,
x = "Number")
openxlsx::writeData(wb = wb.name,
sheet = sheet.name,
startCol = 5,
startRow = 2,
x = "Percentage (%)")
##----- set column widths
openxlsx::setColWidths(wb = wb.name,
sheet = sheet.name,
cols = 1:5,
widths = "auto")
##----- number of digits for "Average conservation"
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.2digits,
cols = c(2, 4),
rows = 7,
gridExpand = TRUE,
stack = TRUE)
##----- number of digits for percentage of clusters with various proportions
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.titles.tables,
cols = c(2:5),
rows = c(1:2),
gridExpand = TRUE,
stack = TRUE)
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.1digits,
cols = c(3, 5),
rows = c(8:13),
gridExpand = TRUE,
stack = TRUE)
##----- number of digits for calculation times
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.comma,
cols = c(2, 4),
rows = c(3:6,14),
gridExpand = TRUE,
stack = TRUE)
##----- number of digits for calculation times
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.4digits,
cols = c(2, 4),
rows = c(16:17),
gridExpand = TRUE,
stack = TRUE)
##----- return the workbook
return(wb.name)
}
## oxWaterOccurrenceSheet docs -------------------------------------------------------
#' @title openxlsx Water Occurrence Summary
#' @description Constructs the [openxlsx] worksheet for the Water Occurrence
#' summary.
#' @details **This function is to _ONLY_ be used with the results of
#' [ConservedWaters()]**. Specific aspects of how the
#' returned `data.frame` will be formatted are **hard-coded** into this
#' function.
#'
#' This [openxlsx] function is _**NOT**_ exported.
#'
#' @param wb.name Name of the workbook for the results; _e.g._, results.wb
#' @param sheet.name Name of the worksheet being formatted; default:
#' `"WaterOccurrenceSummary"`
#' @param df data.frame containing the water occurrence results of the
#' [ConservedWaters()] function; _e.g._, `h2o.occurrence`
#'
#' @return The workbook containing the indicated and newly formatted worksheet.
#'
#' @import openxlsx
#'
#' @author Emilio Xavier Esposito \email{emilio@@exeResearch.com}
#'
#' @family "openxlsx functions"
#'
oxWaterOccurrenceSheet <- function(wb.name,
sheet.name = "WaterOccurrenceSummary",
df) {
##----- data.frame dimensions and other information
df.size <- dim(df)
df.row.idc <- 2:(df.size[1] + 1)
df.col.idc <- 1:(df.size[2] + 1)
df.colnames <- colnames(df)
##----- add sheet
openxlsx::addWorksheet(wb = wb.name,
sheetName = sheet.name,
gridLines = TRUE)
##----- add data
openxlsx::writeDataTable(wb = wb.name,
sheet = sheet.name,
x = as.data.frame(df, stringsAsFactors = FALSE),
colNames = TRUE,
rowNames = TRUE,
tableStyle = "none",
withFilter = FALSE,
headerStyle = cs.header)
##----- freeze the panes
openxlsx::freezePane(wb = wb.name,
sheet = sheet.name,
firstRow = TRUE, firstCol = TRUE)
##----- set column widths
openxlsx::setColWidths(wb = wb.name,
sheet = sheet.name,
cols = df.col.idc,
widths = "auto")
##----- number of digits
##--- the resolution column
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.2digits,
cols = 2,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- the rObserved and rFree columns
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.3digits,
cols = c(3, 4),
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- the means columns
mu.cols.idc <- grep(pattern = ".mu", df.colnames) + 1
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.2digits,
cols = mu.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- the standard deviation columns
sd.cols.idc <- grep(pattern = ".sd", df.colnames) + 1
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.3digits,
cols = sd.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- the percent
pct.cols.idc <- grep(pattern = "pct.", df.colnames) + 1
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.1digits,
cols = pct.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##----- color-code the cluster true-false table
cluster.cols.idc <- grep(pattern = "clust_", df.colnames) + 1
openxlsx::conditionalFormatting(wb = wb.name,
sheet = sheet.name,
cols = cluster.cols.idc,
rows = df.row.idc,
type = "contains",
rule = "TRUE",
style = cs.green)
openxlsx::conditionalFormatting(wb = wb.name,
sheet = sheet.name,
cols = cluster.cols.idc,
rows = df.row.idc,
type = "contains",
rule = "FALSE",
style = cs.pink)
##----- return the workbook
return(wb.name)
}
## oxClusterSummarySheet docs --------------------------------------------------
#' @title openxlsx Cluster Summary Sheet
#' @description Constructs the [openxlsx] worksheet for the Cluster Summary
#' analysis.
#' @details **This function is to _ONLY_ be used with the results of
#' [ConservedWaters()]**. Specific aspects of how the
#' returned `data.frame` will be formatted are **hard-coded** into this
#' function.
#'
#' This [openxlsx] function is _**NOT**_ exported.
#'
#' @param wb.name Name of the workbook for the results; _e.g._, results.wb
#' @param sheet.name Name of the worksheet being formatted; default:
#' `"ClusterSummary"`
#' @param df data.frame containing the cluster summary from the
#' [ConservedWaters()] function; _e.g._, `h2o.clusters.summary`
#'
#' @return The workbook containing the indicated and newly formatted worksheet.
#'
#' @import openxlsx
#'
#' @author Emilio Xavier Esposito \email{emilio@@exeResearch.com}
#'
#' @family "openxlsx functions"
#'
oxClusterSummarySheet <- function(wb.name,
sheet.name = "ClusterSummary",
df) {
##----- data.frame dimensions and other information
df.size <- dim(df)
df.row.idc <- 2:(df.size[1] + 1)
df.col.idc <- 1:df.size[2]
df.colnames <- colnames(df)
##----- add sheet
openxlsx::addWorksheet(wb = wb.name,
sheetName = sheet.name,
gridLines = TRUE)
##----- add data
openxlsx::writeDataTable(wb = wb.name,
sheet = sheet.name,
x = as.data.frame(df, stringsAsFactors = FALSE),
colNames = TRUE,
rowNames = FALSE,
tableStyle = "none",
withFilter = FALSE,
headerStyle = cs.header)
##----- freeze the panes
openxlsx::freezePane(wb = wb.name,
sheet = sheet.name,
firstRow = FALSE, firstActiveRow = 2,
firstCol = FALSE, firstActiveCol = 4)
##----- set column widths
openxlsx::setColWidths(wb = wb.name,
sheet = sheet.name,
cols = df.col.idc,
widths = "auto")
##----- number of digits
##--- the x, y, and z columns
xyz.cols.idc <- which(df.colnames %in% c("x", "y", "z"))
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.3digits,
cols = xyz.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- the calc columns
mu.cols.idc <- grep(pattern = ".calc", df.colnames)
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.2digits,
cols = mu.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- the means columns
mu.cols.idc <- grep(pattern = ".mu", df.colnames)
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.2digits,
cols = mu.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- the standard deviation columns
sd.cols.idc <- grep(pattern = ".sd", df.colnames)
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.3digits,
cols = sd.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- the percent
pct.cols.idc <- grep(pattern = "pct.", df.colnames)
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.1digits,
cols = pct.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- the rmsf column
rmsf.cols.idc <- grep(pattern = "rmsf", df.colnames)
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.4digits,
cols = rmsf.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- the means columns
mobility.cols.idc <- grep(pattern = "mobility", df.colnames)
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.2digits,
cols = mobility.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##----- return the workbook
return(wb.name)
}
## oxRCSBinfoSheet docs --------------------------------------------------
#' @title openxlsx PDB/RCSB Summary Sheet
#' @description Constructs the [openxlsx] worksheet for the Similarity
#' Summary analysis.
#' @details **This function is to _ONLY_ be used with the results of
#' [ConservedWaters()]**. Specific aspects of how the
#' returned `data.frame` will be formatted are **hard-coded** into this
#' function.
#'
#' This [openxlsx] function is _**NOT**_ exported.
#'
#' @param wb.name Name of the workbook for the results; _e.g._, results.wb
#' @param sheet.name Name of the worksheet being formatted; default:
#' "PDB_information"
#' @param df data.frame containing the PDB/RCSB information obtatined within the
#' [ConservedWaters()] function; _e.g._, `pdbs.information`
#'
#' @return The workbook containing the indicated and newly formatted worksheet.
#'
#' @import openxlsx
#'
#' @author Emilio Xavier Esposito \email{emilio@@exeResearch.com}
#'
#' @family "openxlsx functions"
#'
oxRCSBinfoSheet <- function(wb.name,
sheet.name = "RCSB_information",
df) {
##----- data.frame dimensions and other information
df.size <- dim(df)
df.row.idc <- 2:(df.size[1] + 1)
df.col.idc <- 1:df.size[2]
df.colnames <- colnames(df)
##----- add sheet
openxlsx::addWorksheet(wb = wb.name,
sheetName = sheet.name,
gridLines = TRUE)
##----- add data
openxlsx::writeDataTable(wb = wb.name,
sheet = sheet.name,
x = as.data.frame(df, stringsAsFactors = FALSE),
colNames = TRUE,
rowNames = FALSE,
tableStyle = "none",
withFilter = FALSE,
headerStyle = cs.header)
##----- freeze the panes
openxlsx::freezePane(wb = wb.name,
sheet = sheet.name,
firstRow = FALSE, firstActiveRow = 2,
firstCol = FALSE, firstActiveCol = 5)
##----- set column widths
openxlsx::setColWidths(wb = wb.name,
sheet = sheet.name,
cols = df.col.idc,
widths = "auto")
##----- set the date format
depositionDate.idx <- which(df.colnames == "depositionDate")
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.date,
cols = depositionDate.idx,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##----- return the workbook
return(wb.name)
}
## oxInitWaterDataSheet docs ---------------------------------------------------
#' @title Initial Water Data Sheet
#' @description Constructs the [openxlsx] worksheet for the initial water data.
#' @details **This function is to _ONLY_ be used with the results of
#' [ConservedWaters()]**. Specific aspects of how the
#' returned `data.frame` will be formatted are **hard-coded** into this
#' function.
#'
#' This [openxlsx] function is _**NOT**_ exported.
#'
#' @param wb.name Name of the workbook for the results; _e.g._, results.wb
#' @param sheet.name Name of the worksheet being formatted; default:
#' `"InitialWaterData"`
#' @param df data.frame containing the concatenate initial waters with
#' experimental and experimentally derived values obtatined within the
#' [ConservedWaters()] function; _e.g._, `h2o.df`
#'
#' @return The workbook containing the indicated and newly formatted worksheet.
#'
#' @import openxlsx
#'
#' @author Emilio Xavier Esposito \email{emilio@@exeResearch.com}
#'
#' @family "openxlsx functions"
#'
oxInitWaterDataSheet <- function(wb.name,
sheet.name = "InitialWaterData",
df) {
##_ data.frame dimensions and other information -----
df.size <- dim(df)
df.row.idc <- 2:(df.size[1] + 1)
df.col.idc <- 1:(df.size[2] + 1)
df.colnames <- colnames(df)
##_ add sheet -----
openxlsx::addWorksheet(wb = wb.name,
sheetName = sheet.name,
gridLines = TRUE)
##_ add data -----
openxlsx::writeDataTable(wb = wb.name,
sheet = sheet.name,
x = as.data.frame(df, stringsAsFactors = FALSE),
colNames = TRUE,
rowNames = TRUE,
tableStyle = "none",
withFilter = FALSE,
headerStyle = cs.header)
##_ freeze the panes -----
openxlsx::freezePane(wb = wb.name, sheet = sheet.name,
firstRow = TRUE, firstCol = TRUE)
##_ set column widths -----
openxlsx::setColWidths(wb = wb.name, sheet = sheet.name,
cols = df.col.idc, widths = "auto")
##_ number of digits -----
##--- the x, y, and z columns
xyz.cols.idc <- which(df.colnames %in% c("x", "y", "z")) + 1
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.3digits,
cols = xyz.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- atom number column
eleno.cols.idc <- which(df.colnames %in% c("eleno")) + 1
openxlsx::addStyle(wb = wb.name,
sheet = sheet.name,
style = cs.0digits,
cols = eleno.cols.idc,
rows = df.row.idc,
gridExpand = TRUE,
stack = TRUE)
##--- occupation, B-value, mobility, and normalized B-values column
ob.cols.idc <- which(df.colnames %in% c("o","b","mobility","nBvalue")) + 1
openxlsx::addStyle(wb = wb.name, sheet = sheet.name, style = cs.2digits,
cols = ob.cols.idc, rows = df.row.idc,
gridExpand = TRUE, stack = TRUE)
##--- the resolution column
res.col.idc <- grep(pattern = "resolution", df.colnames) + 1
openxlsx::addStyle(wb = wb.name, sheet = sheet.name, style = cs.2digits,
cols = res.col.idc, rows = df.row.idc,
gridExpand = TRUE, stack = TRUE)
##--- the rObserved and rFree columns
res.col.idc <- c(grep(pattern = "rObserved", df.colnames),
grep(pattern = "rFree", df.colnames) ) + 1
openxlsx::addStyle(wb = wb.name, sheet = sheet.name, style = cs.3digits,
cols = c(3, 4), rows = df.row.idc,
gridExpand = TRUE, stack = TRUE)
##--- the summation columns
sum.cols.idc <- grep(pattern = ".sum", df.colnames) + 1
openxlsx::addStyle(wb = wb.name, sheet = sheet.name, style = cs.3digits,
cols = sum.cols.idc, rows = df.row.idc,
gridExpand = TRUE, stack = TRUE)
##--- the means columns
mu.cols.idc <- grep(pattern = ".mu", df.colnames) + 1
openxlsx::addStyle(wb = wb.name, sheet = sheet.name, style = cs.2digits,
cols = mu.cols.idc, rows = df.row.idc,
gridExpand = TRUE, stack = TRUE)
##--- the standard deviation columns
sd.cols.idc <- grep(pattern = ".sd", df.colnames) + 1
openxlsx::addStyle(wb = wb.name, sheet = sheet.name, style = cs.3digits,
cols = sd.cols.idc, rows = df.row.idc,
gridExpand = TRUE, stack = TRUE)
##_ color-code the cluster true-false table -----
tf.cols.idc <- c(grep(pattern = ".keep", df.colnames),
grep(pattern = ".cutoffs", df.colnames) ) + 1
openxlsx::conditionalFormatting(wb = wb.name, sheet = sheet.name,
cols = tf.cols.idc, rows = df.row.idc,
type = "contains", rule = "TRUE",
style = cs.green)
openxlsx::conditionalFormatting(wb = wb.name, sheet = sheet.name,
cols = tf.cols.idc, rows = df.row.idc,
type = "contains", rule = "FALSE",
style = cs.pink)
##_ return the workbook -----
return(wb.name)
}
## oxAlignOverlapSheet docs ----------------------------------------------------
#' @title Align Overlap Data Sheet
#' @description Constructs the [openxlsx] worksheet for the
#' [AlignOverlap()] results.
#' @details **This function is to _ONLY_ be used with the results of
#' [AlignOverlap()]**. Specific aspects of how the
#' returned `data.frame` will be formatted are **hard-coded** into this
#' function.
#'
#' Notable formatting:
#' - Top row frozen
#' - Column widths are set based on column content
#' - Structures passing the [AlignOverlap()] evaluation are hightlighted
#' lime green
#' - Structures failing the [AlignOverlap()] evaluation are hightlighted
#' pink
#'
#' This [openxlsx] function is _**NOT**_ exported.
#'
#' @param wb.name Name of the workbook for the results; _e.g._, results.wb
#' @param sheet.name Name of the worksheet being formatted; default:
#' `"AlignOverlap"`
#' @param df data.frame containing the summary of [AlignOverlap()]; _e.g._,
#' `df.results`
#'
#' @return The workbook containing the indicated and newly formatted worksheet.
#'
#' @import openxlsx
#'
#' @author Emilio Xavier Esposito \email{emilio@@exeResearch.com}
#'
#' @family "openxlsx functions"
#'
oxAlignOverlapSheet <- function(wb.name,
sheet.name = "AlignOverlap",
df) {
##----- data.frame dimensions and other information
df.size <- dim(df)
df.row.idc <- 2:(df.size[1] + 1)
df.col.idc <- 1:(df.size[2] + 1)
df.colnames <- colnames(df)
##----- add sheet
openxlsx::addWorksheet(wb = wb.name,
sheetName = sheet.name,
gridLines = TRUE)
##----- add data
openxlsx::writeDataTable(wb = wb.name,
sheet = sheet.name,
x = as.data.frame(df, stringsAsFactors = FALSE),
colNames = TRUE,
rowNames = FALSE,
tableStyle = "none",
withFilter = FALSE,
headerStyle = cs.header)
##----- freeze the panes
openxlsx::freezePane(wb = wb.name,
sheet = sheet.name,
firstRow = TRUE,
firstCol = FALSE)
##----- set column widths
openxlsx::setColWidths(wb = wb.name,
sheet = sheet.name,
cols = df.col.idc,
widths = "auto")
##----- color-code the cluster true-false table
openxlsx::conditionalFormatting(wb = wb.name,
sheet = sheet.name,
cols = c(2, 5),
rows = df.row.idc,
type = "contains",
rule = "TRUE",
style = cs.green)
openxlsx::conditionalFormatting(wb = wb.name,
sheet = sheet.name,
cols = c(2, 5),
rows = df.row.idc,
type = "contains",
rule = "FALSE",
style = cs.pink)
##----- return the workbook
return(wb.name)
}
## oxPDBcleanedSummarySheet docs -----------------------------------------------
#' @title Cleaned PDB Structures Data Sheet
#' @description Constructs the [openxlsx] worksheet for the
#' [CleanProteinStructures()] results.
#' @details **This function is to _ONLY_ be used with the results of
#' [CleanProteinStructures()]**. Specific aspects of how the
#' returned `data.frame` will be formatted are **hard-coded** into this
#' function.
#'
#' Notable formatting:
#' - Top row frozen
#' - Column widths are set based on column content
#' - Structures with hydrogen atoms removed are highlighted with amber cell color
#' - Structures with OoR values, modeled atoms, and removed waters are highlighted
#' with amber cell color
#'
#' This [openxlsx] function is _**NOT**_ exported.
#'
#' @param wb.name Name of the workbook for the results; _e.g._, results.wb
#' @param sheet.name Name of the worksheet being formatted; default:
#' `"PDBcleanedSummary"`
#' @param df data.frame containing the summary of
#' [CleanProteinStructures()]; _e.g._, `df.results`
#'
#' @return The workbook containing the indicated and newly formatted worksheet.
#'
#' @import openxlsx
#'
#' @author Emilio Xavier Esposito \email{emilio@@exeResearch.com}
#'
#' @family "openxlsx functions"
#'
oxPDBcleanedSummarySheet <- function(wb.name,
sheet.name = "PDBcleanedSummary",
df) {
##----- data.frame dimensions and other information
df.size <- dim(df)
df.row.idc <- 2:(df.size[1] + 1)
df.col.idc <- 1:(df.size[2] + 1)
df.colnames <- colnames(df)
##----- add sheet
openxlsx::addWorksheet(wb = wb.name,
sheetName = sheet.name,
gridLines = TRUE)
##----- add data
openxlsx::writeDataTable(wb = wb.name,
sheet = sheet.name,
x = as.data.frame(df, stringsAsFactors = FALSE),
colNames = TRUE,
rowNames = FALSE,
tableStyle = "none",
withFilter = FALSE,
headerStyle = cs.header)
##----- freeze the panes
openxlsx::freezePane(wb = wb.name,
sheet = sheet.name,
firstRow = TRUE,
firstCol = FALSE)
##----- set column widths
openxlsx::setColWidths(wb = wb.name,
sheet = sheet.name,
cols = df.col.idc,
widths = "auto")
##----- color structures with removed hydrogens amber
openxlsx::conditionalFormatting(wb = wb.name,
sheet = sheet.name,
cols = c(2),
rows = df.row.idc,
type = "contains",
rule = "TRUE",
style = cs.amber)
##----- color values for structures with OoR values, modeled atoms, and
## removed waters
openxlsx::conditionalFormatting(wb = wb.name,
sheet = sheet.name,
cols = c(3, 4, 5),
rows = df.row.idc,
type = "expression",
rule = "!=0",
style = cs.amber)
openxlsx::conditionalFormatting(wb = wb.name,
sheet = sheet.name,
cols = c(7),
rows = df.row.idc,
type = "expression",
rule = "!=0",
style = cs.amber)
##----- return the workbook
return(wb.name)
}
## oxPlainDataSheet docs -------------------------------------------------------
#' @title Plain Data Sheet
#' @description Constructs a plain Excel worksheet via the [openxlsx] package.
#' @details **This function creates a basic Excel worksheet with minimal
#' formatting.**
#'
#' Notable formatting:
#' - Top row frozen
#' - Column widths are set based on column content
#'
#' This [openxlsx] function is _**NOT**_ exported.
#'
#' @param wb.name Name of the workbook for the results; _e.g._, results.wb
#' @param sheet.name Name of the worksheet being formatted; default:
#' `"basic"`
#' @param df data.frame containing the data to be written; _e.g._, `df.results`
#'
#' @return The workbook containing the indicated and newly formatted worksheet.
#'
#' @import openxlsx
#'
#' @author Emilio Xavier Esposito \email{emilio@@exeResearch.com}
#'
#' @family "openxlsx functions"
#'
oxPlainDataSheet <- function(wb.name,
sheet.name = "basic",
df) {
##----- data.frame dimensions and other information
df.size <- dim(df)
df.row.idc <- 2:(df.size[1] + 1)
df.col.idc <- 1:(df.size[2] + 1)
df.colnames <- colnames(df)
##----- add sheet
openxlsx::addWorksheet(wb = wb.name,
sheetName = sheet.name,
gridLines = TRUE)
##----- add data
openxlsx::writeDataTable(wb = wb.name,
sheet = sheet.name,
x = as.data.frame(df, stringsAsFactors = FALSE),
colNames = TRUE,
rowNames = FALSE,
tableStyle = "none",
withFilter = FALSE,
headerStyle = cs.header)
##----- freeze the panes
openxlsx::freezePane(wb = wb.name,
sheet = sheet.name,
firstRow = TRUE,
firstCol = TRUE)
##----- set column widths
openxlsx::setColWidths(wb = wb.name,
sheet = sheet.name,
cols = df.col.idc,
widths = "auto")
##----- return the workbook
return(wb.name)
}
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