loopplotexp: Plot all NTB experiments into one single PDF

In volkmannp/ntbgraphics: Visualization of NTB Data

Description

A function that takes an NTB dataset and visualizes the data as customized boxplots, saving it into one PDF file. Requires functions 'ploteachexp' and 'getexpdata' internally. For right formatting of your files, please consider the "ReadMe for ntbgraphics".

Usage

loopplotexp(
  directory,
  analysis = c("2arm_ko", "2arm_tg", "2arm_sd", "2arm_treat", "4arm_sd_ko",
    "4arm_sd_tg", "4arm_treat_ko", "4arm_treat_tg"),
  ordercolumns = c("ntb", "rdoc", "manual"),
  ordercolumns_manual = FALSE,
  exclude.animals = FALSE,
  orderlevelcond = c("other", "gtblock", "etblock", "2rev"),
  acceptable.nas = "unlimited",
  saveplotdir = directory
)

Arguments

directory	specifies file directory of 'Meta Behavior' and 'Animal List' files within quotation marks (mind correct spelling of both files and 'directory'!); no default
analysis	specifies the kind of experiment performed within quotation marks; "2arm_ko","2arm_tg", "2arm_sd", "2arm_treat", "4arm_sd_ko", "4arm_sd_tg", "4arm_treat_ko", "4arm_treat_tg" (tg for transgenic, ko for knockout; 4arm_sd_x assumes a stress paradigm with social defeat (sd) and housing or handling control (hc) as control; 4arm_treat_x assumes a treatment paradigm with treated (treat) and untreated (untreat) animals; 2arm_x assumes wildtype controls (wt) for tg and ko, housing or handling controls (hc) for sd and untreated controls (untreat) for treated animals; ('analysis' defines the kind of experiment performed, respectively the kind of analysis preferred - you can easily perform 2arm analysis for 4arm experiments looking only at the groups of interest, but not the other way around); default: "2arm_ko"
ordercolumns	defines the order paradigm of experiment (column) appearance in internal table and final PDF file within quotation marks: "ntb", "rdoc", "manual"; order of experiments may be chronological with "ntb", follow RDoC clustering with "rdoc" or be customized manually with "manual" (-> use 'ordercolumns_manual' for exact appearance; there, you may also choose to exclude experiments); default: "ntb"
ordercolumns_manual	customizes order of appearance and appearance itself of experiment columns in internal table and final PDF file (experiments that are not listed will not be included); only if 'ordercolumns' = "manual"; user has to provide a vector containing characters within quotation marks (e.g. by using c("Meanspeed", "SerialLearn")) with all experiments he wants to include into the experiment selection with desired order; no need for specification if 'ordercolumns' is not "manual" default: FALSE
exclude.animals	excluding animals from analysis by RFID; user has to provide a vector containing characters within quotation marks (e.g. by using c("900200000067229", "900200000065167")) with all animals he wants to exclude from the final plotting; if FALSE is provided, no animal will be excluded; default: FALSE
orderlevelcond	defines order of boxplots in plot within quotation marks: "other", "gtblock", "etblock", "2rev"; "other" for alphabetical order in case of 4arm; also for default order of 2arm experiments (which displays the 'control' first, then the 'condition'); "gtblock" for order wt_x, wt_y, tg_x, tg_y; "etblock" for order x_hc, y_hc, x_sd, y_sd; "2rev" for inverse order of 2arm default only, meaning displaying the 'condition' first, then the 'control'; default: "other"
acceptable.nas	defines the maximum number of NAs allowed within the same row; if number of actual NAs within one row is bigger than the number provided, the row will be excluded from table and following plotting; if the number of acceptable NAs should be unlimited, no value has to be provided; default: "unlimited"
saveplotdir	file directory where to save plots; default: location of Behavior and Animal List files as specified in 'directory'

Value

all boxplots saved in one PDF

Author(s)

Paul Volkmann

Examples

loopplotexp(paste0(system.file("extdata", package = "ntbgraphics", mustWork = T),"/"))

loopplotexp(directory = paste0(system.file("extdata", package = "ntbgraphics", mustWork = T),"/"),
                     analysis = "4arm_sd_tg",
                     ordercolumns = "ntb",
                     exclude.animals = c("900200000068816"),
                     orderlevelcond = "etblock",
                     acceptable.nas = 2,
                     saveplotdir = paste0(system.file("../plots", package = "ntbgraphics", mustWork = T),"/"))

volkmannp/ntbgraphics documentation built on March 3, 2020, 1:25 p.m.