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report.Rmd
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report.Rmd
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---
#title: "Metadata Checklist"
#author: "Rebecca Senft"
#date: "1/30/2021"
header-includes:
- \usepackage[default]{sourcesanspro}
- \usepackage[T1]{fontenc}
- \usepackage{xcolor}
- \usepackage{leading}
mainfont: SourceSansPro
output: pdf_document
params:
Metadata: Metadata
examples: examples
modality: modality
Q1: Q1
Q1b: Q1b
Q1c: Q1c
Q2: Q2
Q3: Q3
Q4: Q4
Q5: Q5
Q6: Q6
Q7: Q7
Q8: Q8
Q9: Q9
Q10: Q10
showExamples: FALSE
# Unfortunately, there is a lot of duplication here as I haven't found a way to pass a lot of text dependent on user input into the params list. So this r markdown file re-generates the metadata checklist conditional on rShiny user input.
# note that $\Box$ doesn't work and in rMarkdown, "- [ ] myLabel" also doesn't work so I used images for checkboxes
# note an alternative for titles: \centerline{\color{white}\colorbox{black}{Universal Metadata}}\\
# text color example: Roses are \textcolor{red}{dd}, violets are \textcolor{blue}{blue}
---
\definecolor{cornflower}{rgb}{0.39,0.58,0.93}
\newcommand\italicblue[1]{\textcolor{cornflower}{\textit{#1}}}
\leading{14pt}
\raggedright
```{r setup, include=FALSE}
library(pander)
panderOptions('knitr.auto.asis', FALSE)
boxSym = "![](checkbox.png){width=1.7%}"
Metadata = params$Metadata
examples= params$examples
#Metadata=read.delim("Metadata_new.txt", header = TRUE, stringsAsFactors = FALSE, na = "", sep = "\t")
#examples=read.delim("examples_new.txt", header = TRUE, stringsAsFactors = FALSE, na="", sep = "\t")
```
\noindent\centerline{\Large{Microscopy Metadata Checklist}}
\noindent\centerline{*** Asterisks indicate optional items}
\par \vspace{4mm}
```{r, echo=FALSE, results='asis'}
knitr::opts_chunk$set(echo = TRUE)
library(stringr)
showExamples=params$showExamples
#function to append to checklist
appendChecklist <- function(input, colName, showExamples) {
output <- ""
if(showExamples==TRUE){
for (i in 1:length(colName)) {
output <- gsub("%", "\\%", na.omit(examples[[colName]]),fixed=TRUE)
output <- gsub("#", "\\#", output,fixed=TRUE)
output <- gsub("^", "\\textasciicircum", output,fixed=TRUE)
output <- paste0(boxSym, "\\space\\space ", na.omit(Metadata[[colName]]),"\\space\\space\\space\\space", "\\italicblue{",output,"} \\newline")
}
}
else{
for (i in 1:length(colName)) {
output <- paste0(output, boxSym, "\\space\\space ", na.omit(Metadata[[colName]]),"\\","newline")
}
}
output <- str_replace_all(paste(output),"\"","")
output <- str_replace_all(output,'\\*\\*\\*','\\\\*\\\\*\\\\* ')#stop r markdown from displaying asterisks as bold italic
output <- append(input,output)
return(output)
}
sortItems <-function(str_list){
sortedlist <- c()
hold <- c()
for(item in str_list){
if(grepl("\\*\\*\\* ", item, fixed=TRUE)){
hold <- append(hold, item)
}
else{
sortedlist <- append(sortedlist, item)
}
}
return(append(sortedlist,hold))}
```
\par\vspace{-4mm}\noindent\color{white}\colorbox{black}{\strut\makebox[\dimexpr \linewidth-2\fboxsep][c]{Microscope Stand and Motorized Components}}\color{black}\vspace{1mm}
```{r, echo=FALSE, results='asis'}
##### General Stand and Motorized Components
all = ""
all <- appendChecklist(all, "all_Stand", showExamples)
if (length(params$Q4)>0 | (params$Q5)=="Y" | (params$Q6)=="Y"){
all <-appendChecklist(all, "Zstack_multiPoint_timeLapse_Stand",showExamples)
}
if ("wheel" %in% (params$Q1b) | ((params$Q1)!="no_input" & (params$Q1)!="WF")){
all <-appendChecklist(all, "emissionWheel_Stand", showExamples)
}
cat(paste(sortItems(all)))
```
```{r, echo=FALSE, results='asis'}
##### Microscope Specific-Stand and Motorized Components
if (params$Q1 %in% c("SConfocal","PConfocal","MPhoton")){
cat(paste0("\\par\\vspace{-8mm}\\noindent\\color{white}\\colorbox{black}{\\strut\\makebox[\\dimexpr \\linewidth-2\\fboxsep][c]{",params$modality,"-Specific Hardware and Settings}}\\color{black}\\vspace{1mm}"))
}
all = ""
if ((params$Q1)=="SConfocal") {
all <-appendChecklist(all, "Sconfocal_Stand", showExamples)
}
if ((params$Q1)=="PConfocal") {
all <-appendChecklist(all, "Pconfocal_Stand", showExamples)
}
if ((params$Q1)=="MPhoton") {
all <-appendChecklist(all, "Mphoton_Stand", showExamples)
}
cat(paste(sortItems(all)))
```
\par\vspace{-8mm}\noindent\color{white}\colorbox{black}{\strut\makebox[\dimexpr \linewidth-2\fboxsep][c]{Illumination}}\color{black}\vspace{1mm}
```{r, echo=FALSE, results='asis'}
knitr::opts_chunk$set(echo = TRUE)
all = ""
if ((params$Q1)=="WF" & "LEDs" %in% (params$Q1c)) {
all <- appendChecklist(all, "WF_nolaser_Illumination", showExamples)
}
if ((params$Q1)=="WF" & "Lasers" %in% (params$Q1c)) {
all <- appendChecklist(all, "WF_laser_Illumination", showExamples)
}
if ((params$Q1)=="SConfocal" & "Lasers" %in% (params$Q1c)) {
all <- appendChecklist(all, "Sconfocal_laser_Illumination", showExamples)
}
if ((params$Q1)=="SConfocal" & "LEDs" %in% (params$Q1c)) {
all <- appendChecklist(all, "Sconfocal_LED_Illumination", showExamples)
}
if ((params$Q1)=="PConfocal") {
all <- appendChecklist(all, "Pconfocal_Illumination", showExamples)
}
if ((params$Q1)=="MPhoton") {
all <- appendChecklist(all, "Mphoton_Illumination", showExamples)
}
cat(paste(sortItems(all)))
```
\par\vspace{-8mm}\noindent\color{white}\colorbox{black}{\strut\makebox[\dimexpr \linewidth-2\fboxsep][c]{Wavelength Selection}}\color{black}\vspace{1mm}
```{r, echo=FALSE, results='asis'}
knitr::opts_chunk$set(echo = TRUE)
all = ""
all <- appendChecklist(all, "All_Wave", showExamples)
if ((params$Q1)=="WF" & "cube" %in% (params$Q1b)) {
all <- appendChecklist(all, "WF_filterCube_Wave", showExamples)
}
cat(paste(sortItems(all)))
```
\par\vspace{-8mm}\noindent\color{white}\colorbox{black}{\strut\makebox[\dimexpr \linewidth-2\fboxsep][c]{Optics}}\color{black}\vspace{1mm}
```{r, echo=FALSE, results='asis'}
knitr::opts_chunk$set(echo = TRUE)
all = ""
all <- appendChecklist(all, "all_Optics", showExamples)
if ((params$Q2)=="Y") {
all <- appendChecklist(all, "transmitted_Optics", showExamples)
}
if ((params$Q3)=="Y") {
all <- appendChecklist(all, "mag_Optics", showExamples)
}
all <- str_replace_all(all,"character(0)","")
cat(paste(sortItems(all)))
```
\par\vspace{-8mm}\noindent\color{white}\colorbox{black}{\strut\makebox[\dimexpr \linewidth-2\fboxsep][c]{Detection}}\color{black}\vspace{1mm}
```{r, echo=FALSE, results='asis'}
knitr::opts_chunk$set(echo = TRUE)
all = ""
if ((params$Q1)=="WF") {
all <- appendChecklist(all, "WF_Detection", showExamples)
}
if ((params$Q1)=="SConfocal") {
all <- appendChecklist(all, "Sconfocal_Detection", showExamples)
}
if ((params$Q1)=="PConfocal") {
all <- appendChecklist(all, "Pconfocal_Detection", showExamples)
}
if ((params$Q1)=="MPhoton") {
all <- appendChecklist(all, "Mphoton_Detection", showExamples)
}
cat(paste(sortItems(all)))
```
\par\vspace{-8mm}\noindent\color{white}\colorbox{black}{\strut\makebox[\dimexpr \linewidth-2\fboxsep][c]{Acquisition Software}}\color{black}\vspace{1mm}
```{r, echo=FALSE, results='asis'}
knitr::opts_chunk$set(echo = TRUE)
all = ""
all <- appendChecklist(all, "all_Software", showExamples)
if (length(params$Q4)>0) {
all <- appendChecklist(all, "multiDim_Software", showExamples)
}
if ("multi-color" %in% (params$Q4)) {
all <- appendChecklist(all, "multiColor_Software", showExamples)
}
if ("z-stack" %in% (params$Q4)) {
all <- appendChecklist(all, "Z_stack_Software", showExamples)
}
if ("time-lapse" %in% (params$Q4)) {
all <- appendChecklist(all, "timeLapse_Software", showExamples)
}
if((params$Q6)=="Y"){
all <- appendChecklist(all, "timeLapse_Software", showExamples)
}
cat(paste(sortItems(all)))
```
\par\vspace{-8mm}\noindent\color{white}\colorbox{black}{\strut\makebox[\dimexpr \linewidth-2\fboxsep][c]{Sample Preparation}}\color{black}\vspace{1mm}
```{r, echo=FALSE, results='asis'}
knitr::opts_chunk$set(echo = TRUE)
all = ""
all <- appendChecklist(all, "all_Sample", showExamples)
if ((params$Q7)=="Y") {
all <- appendChecklist(all, "live_Sample", showExamples)
} else if((params$Q7)=="N"){
all <- appendChecklist(all, "fixed_Sample", showExamples)
}
if ("FP" %in% (params$Q8)) {
all <- appendChecklist(all, "FP_Sample", showExamples)
}
if ("Dye" %in% (params$Q8)) {
all <- appendChecklist(all, "dye_Sample", showExamples)
}
if ((params$Q9)=="Y") {
all <- appendChecklist(all, "transfect_Sample", showExamples)
}
cat(paste(sortItems(all)))
```
\par\vspace{-8mm}\noindent\color{white}\colorbox{black}{\strut\makebox[\dimexpr \linewidth-2\fboxsep][c]{Acknowledgements}}\color{black}\vspace{1mm}
```{r, echo=FALSE, results='asis'}
knitr::opts_chunk$set(echo = TRUE)
all = ""
if ((params$Q10)=="Y") {
all <- appendChecklist(all, "core_Ack", showExamples)
}
cat(paste(sortItems(all)))
```
\vfill
\noindent For more information, check out our paper: Montero-Llopis et al., 2021 (citation)
\noindent Microscopy Metadata Checklist Generator (MicCheck) developed by Rebecca Senft (2021)