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This updates `process_raw_data.R` to process all data in `root/data-raw/results_csv`. Some work is still needed to properly update the database at `.data/chemo-dash.sqlite`
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| # process_19000101_data.R | ||
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| library(ChemotaxisDashboard) | ||
| library(magrittr) | ||
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| # start up parallel back end | ||
| parallel::makeCluster(parallel::detectCores() - 1, | ||
| type = "PSOCK" | ||
| ) %>% | ||
| doParallel::registerDoParallel() | ||
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| # process test data | ||
| processed_data <- process_experiments('19000101', | ||
| source_dir = system.file("extdata", package = "ChemotaxisDashboard"), | ||
| results_dir = file.path(system('git rev-parse --show-toplevel', intern = TRUE), '.data'), | ||
| seed = 923847) | ||
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| ##################################### | ||
| # data.frames for RSQLite db tables # | ||
| ##################################### | ||
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| #' users | ||
| #' User table for authentication | ||
| #' | ||
| #' @param user Character, username - used in: | ||
| #' `access` | ||
| #' @param password Character, password | ||
| users <- data.frame(user = "shinyuser", # default user | ||
| password = "12345") | ||
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| #' access | ||
| #' User access table defining which experiments the user can access | ||
| #' | ||
| #' @param user Character, maps to `users$user` | ||
| #' @param expID Character, maps to `expSummary$expID` | ||
| access <- data.frame(user = "shinyuser", | ||
| expID = "19000101") # default user has access to test data only | ||
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| #' expSummary | ||
| #' Experiment summary table | ||
| #' | ||
| #' @param expID Character, experiment ID - used in: | ||
| #' `access` | ||
| #' `expStats` | ||
| #' `chanSummary` | ||
| #' `chanRaw` | ||
| #' `trackSummary` | ||
| #' `trackRaw` | ||
| #' @param tracks_time Character, path to figure of tracks over time for each channel | ||
| #' @param tracks_v Character, path to figure of velocity over time for each grouping | ||
| #' @param angle_migration Character, path to figure of angle of migration viloin plots for each channel | ||
| #' @param ce Character, path to figure of chemotactic efficiency violin plots for each channel | ||
| expSummary <- processed_data$expSummary | ||
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| #' expStats | ||
| #' Table of summary statistics for each experiment | ||
| #' | ||
| #' @param expID Character, maps to `expSummary$expID` | ||
| #' @param within Character, group for the comparison (i.e. within normals treated with fMLF8) | ||
| #' @param between Character, contrast for the comparison (i.e. between channels 3 and 4) | ||
| #' @param test Character, test used to compare the `between` groups | ||
| #' @param stat Double, test statistics comparing the `between` groups | ||
| #' @param p Double, p-value for `stat` | ||
| expStats <- processed_data$expStats | ||
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| #' chanSummary | ||
| #' Channel summary table | ||
| #' | ||
| #' @param expID Character, maps to `expSummary$expID` | ||
| #' @param chanID Integer, channel ID - used in: | ||
| #' `chanRaw` | ||
| #' `trackRaw` | ||
| #' `trackSummary` | ||
| #' @param sID Character, sample ID - used in: | ||
| #' @param treatment Character, treatment applied to this channel | ||
| #' @param tot_finished Integer, Total number of cells that reached the bottom ledge | ||
| #' @param prop_finished Double, proportion of cells that reached the bottom ledge | ||
| #' @param ce_median Double, median chemotactic efficiency | ||
| #' @param ce_mean Double, mean chemotactic efficiency | ||
| #' @param ce_sd Double, standard deviation of chemotactic efficiency | ||
| #' @param angle_median Double, median angle of migration | ||
| #' @param angle_mean Double, mean angle of migration | ||
| #' @param angle_sd Double, standard deviation of angle of migration | ||
| #' @param max_v_median Double, median maximum velocity | ||
| #' @param max_v_mean Double, mean maximum velocity | ||
| #' @param max_v_sd Double, standard deviation of maximum velocity | ||
| #' @param dvud Double, dissimilarity score comparing directed and undirected trajectories | ||
| #' @param dvud_p Double, p-value for `dvud` | ||
| chanSummary <- processed_data$chanSummary | ||
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| #' chanRaw | ||
| #' Table of smoothed trajectories over all tracks in a channel | ||
| #' | ||
| #' @param expID Character, maps to `expSummary$expID` | ||
| #' @param chanID Integer, maps to `chanSummary$chanID` | ||
| #' @param x Double, smoothed x-position for the channel | ||
| #' @param y Double, smoothed y-position for the channel | ||
| #' @param frames Integer, frame (sampled every 30 seconds) | ||
| #' @param v_x Double, velocity in the x direction (undirected) | ||
| #' @param v_y Double, velocity in the y direction (directed) | ||
| #' @param v Double, total velocity | ||
| chanRaw <- processed_data$chanRaw | ||
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| #' trackSummary | ||
| #' Track summary table | ||
| #' | ||
| #' @param expID Character, maps to `expSummary$expID` | ||
| #' @param chanID Integer, maps to `chanSummary$chanID` | ||
| #' @param trackID Integer, track ID - used in: | ||
| #' `trackRaw` | ||
| #' @param ce Double, chemotactic efficiency | ||
| #' @param angle_migration Double, angle of migration | ||
| #' @param max_v Double, maximum velocity in μm per minute | ||
| #' @param av_velocity Double, mean velocity in μm per minute | ||
| #' @param finished Logical, TRUE when the cell passed the bottom ledge | ||
| trackSummary <- processed_data$trackSummary | ||
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| #' trackRaw | ||
| #' Raw track information | ||
| #' | ||
| #' @param expID Character, maps to `expSummary$expID` | ||
| #' @param chanID Integer, maps to `chanSummary$chanID` | ||
| #' @param trackID Integer, maps to `trackSummary$trackID` | ||
| #' @param x Double, x-position for the track | ||
| #' @param y Double, y-position for the track | ||
| #' @param frames Integer, frame (sampled every 30 seconds) | ||
| #' @param v_x Double, velocity in the x direction (undirected) | ||
| #' @param v_y Double, velocity in the y direction (directed) | ||
| #' @param v Double, total velocity | ||
| trackRaw <- processed_data$trackRaw | ||
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| # export for internal use | ||
| usethis::use_data(users, | ||
| access, | ||
| expSummary, | ||
| expStats, | ||
| chanSummary, | ||
| chanRaw, | ||
| trackSummary, | ||
| trackRaw, | ||
| internal = TRUE, overwrite = TRUE) |
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