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config.yml
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default:
# == FILE AND NETWORK PATHS == #
# -- Local Files -- #
# All file system paths are relative to "main.R".
data_directory: "data/"
output_directory: "output/"
morphometrics_name: "density_morphometrics"
count_control_name: "density_counts"
data_extension: ".csv"
figure_2_name: "Fig_2"
figure_3_name: "Fig_3"
figure_4_name: "Fig_4"
figure_5_name: "Fig_5"
figure_S1_name: "Fig_S1"
figure_extension: ".svg" # This will also determine the output format.
table_1_name: "Table_1"
table_2_name: "Table_2"
table_S1_name: "Table_S1"
table_S2_name: "Table_S2"
table_S3_name: "Table_S3"
table_S4_name: "Table_S4"
table_S5_name: "Table_S5"
count_table_name: "Count_Control_Table"
table_extension: ".html" # This will also determine the output format.
# -- Remote Files and Local Paths to Store Them -- #
# NB: As the file is not yet on the database, the URL here is just an
# educated guess.
database_path_prefix: "http://dmoserv3.bco-dmo.org/jg/serv/BCO-DMO/LIPs_on_Larval_Feeding/"
database_path_suffix: ".flat0?"
download_morphometrics: true
download_count_control: true
overwrite_on_download: false
morphometrics_min_expected_bytes: 500 # Probably >60K, but use lower limit in case compressed or something.
count_control_min_expected_bytes: 500 # Probably ~2K, but use lower limit in case compressed or something.
# == OUTPUT SELECTION == #
# These settings control which figures and tables should be generated.
# NB: There is no Figure 1 in this list as it is an illustration, not a plot.
make_figure_2: true
make_figure_3: true
make_figure_4: true
make_figure_5: true
make_figure_S1: true
make_table_1: true
make_table_2: true
make_table_S1: true
make_table_S2: true
make_table_S3: true
make_table_S4: true
make_table_S5: true
make_count_table: true
# -- Post Processing Options -- #
postprocess: true # Runs Python script to pretty up the output.
postprocess_suffix: "" # If empty, overwrite original with pretty output.
postprocess_soup: true # Use bs4 Beautiful Soup module.
# == INPUT FORMAT == #
# -- CSV Column Names -- #
col_spawn_date: "Spawn_date"
col_species: "Species"
col_experiment: "Experiment"
col_beaker: "Beaker"
col_density: "Culture_density"
col_food: "Food"
col_bl: "Midline_body_length"
col_po: "Right_PO_arm_length"
col_sl: "Stomach_length"
col_age: "Age"
col_stage: "Stage"
col_image: "Image"
col_counted: "Larvae_counted"
col_expected: "Larvae_expected"
# -- CSV Factor Levels. -- #
species_level_dend: "Dendraster excentricus"
species_level_lyt: "Lytechinus pictus"
experiment_level_dend1: "D. excentricus Expt 1"
experiment_level_dend2: "D. excentricus Expt 2"
experiment_level_lyt1: "L. pictus Expt 1"
experiment_level_lyt2: "L. pictus Expt 2"
density_level_extrasparse: "0.015"
density_level_sparse: "0.05"
density_level_dense: "0.25"
food_level_low: "250"
food_level_high: "5000"
# == ANALYSIS SETTINGS == #
# Threshold values for statistical tests.
shapiro_p: 0.05
levene_p: 0.05
anova_p: 0.05
# == OUTPUT FORMAT == #
# -- Display Names for Plot Legends, Table Headers, etc. -- #
spawn_date_label_col_header: "Spawn Date"
proportion_label_col_header: "Proportion of Nominal"
species_label_col_header: "Species"
experiment_label_col_header: "Experiment"
experiment_label_dend1: "D. excentricus Expt 1"
experiment_label_dend2: "D. excentricus Expt 2"
experiment_label_lyt1: "L. pictus Expt 1"
experiment_label_lyt2: "L. pictus Expt 2"
density_label_extrasparse: "0.015"
density_label_sparse: "0.05"
density_label_dense: "0.25"
density_label_legend: "Density (larvae/ml)"
density_label_col_header: "Culture Density (larvae/ml)"
food_label_low: "250"
food_label_high: "5,000"
food_label_legend: "Food (cells/ml)"
food_label_col_header: "Food Ration (cells/ml)"
po_label: "PORL (μm)"
po_label_no_units: "PORL"
po_emm_label: "EMM for PORL (μm)"
po_lmem_label: "LMEM for PORL (μm)"
po_bl_ratio_label: "PORL/BL"
sl_label: "SL (μm)"
sl_label_no_units: "SL"
sl_emm_label: "EMM for SL (μm)"
bl_emm_label: "EMM for BL (μm)"
sl_lmem_label: "LMEM for SL (μm)"
sl_bl_ratio_label: "SL/BL"
bl_label: "BL (μm)"
# -- Graphical Representations: Color, Fill, and Shape -- #
food_color_low: "#ffffff" # White.
food_color_high: "#6081bf" # Blue.
density_shape_extrasparse: 25 # ▼ Downward-facing triangle, filled.
density_shape_sparse: 21 # ● Circle, filled.
density_shape_dense: 24 # ▲ Upward-facing triangle, filled.
density_shape_size: 3
density_stroke: 1 # Slightly thicker stroke width.
density_line_color: "#000000" # Black.
error_bar_color: "#000000" # Black.
# -- Plot Axis Scales -- #
figure_2_bl_y_max: 400
figure_2_po_y_max: 410
figure_2_sl_y_max: 150
figure_3_y_max: 450
figure_4_y_max: 150
figure_S1_po_bl_ratio_y_max: 1.7
figure_S1_sl_bl_ratio_y_max: 0.5
# -- Plot Element Positioning -- #
figure_2_bar_dodge: 0.8
figure_3_4_bar_dodge: 0.8
figure_S1_bar_dodge: 0.8
# Height of stars/p-values relative to bar height.
figure_2_star_height_mult: 1.05
figure_3_4_p_height_mult: 1.05
figure_S1_height_mult: 1.05
figure_3_4_error_width: 0.2
figure_S1_error_width: 0.2
figure_5_legend_spacing_mm: 1.0 # Squish legends to fit.
# -- Plot Output File Dimensions --#
# These are based on MEPS guidelines.
figure_2_width_mm: 169
figure_2_height_mm: 169
figure_3_width_mm: 169
figure_3_height_mm: 88.556
figure_4_width_mm: 169
figure_4_height_mm: 88.556
figure_5_width_mm: 169
figure_5_height_mm: 88.556
figure_S1_width_mm: 169
figure_S1_height_mm: 169
p_value_font_size: 3 # 3.88 is ggpubr default. Units = ??
# -- Number/Star Formatting -- #
p_value_nsmall: 3 # Digits past zero to show.
p_value_max_cutoff: 0.05 # Don't print p >= this.
p_value_min_cutoff: 0.001 # Print p < this as "p<(p_value_min_cutoff)".
table_digits: 3
p_star_cut_triple: 0.001
p_star_cut_double: 0.01
p_star_cut_single: 0.05
# == CONSOLE OUTPUT == #
warn_singular: false # Print warnings for singular LMEMs.
warn_multcomp: false # Print warnings from multcomp.
break_on_warning: false