# IMPORTANT: before trying to generate the superplot
# Users must change the "filename" and "data_format" arguments if using an "untidy" format. If the format is tidy,
# also change "condition", "value", and "replicate" to match the column names in your dataset.
# X and Y labels will not be plotted by default. Change these arguments according to your preference.

# csv file or Microsoft Excel file containing data in tidy data format. Include file extension in the name
filename: REPLACE_ME

# tidy or untidy format. Refer to documentation for more information
data_format: tidy

# the label for the x axis. To have no label on the x axis, don't change the default value.
xlabel: REPLACE_ME

# label for the y axis. To have no label on the y axis, don't change the default value.
ylabel: REPLACE_ME

# variable to display on the x axis
condition: REPLACE_ME

# variable to display on the y axis
value: REPLACE_ME

# variable used to denote experimental replicates
replicate: REPLACE_ME


# The following arguments below may be changed as the user desires

# order of the experimental conditions from left to right
# must be separated by ", " e.g. Control, Drug
order: None

# use mean (default) or median to position the scatterpoints over each replicate
centre_val: mean

# use mean or median from each experimental replicate.
# Used to calculate the centre_val. Default: mean
middle_vals: mean

# standard error of the mean (SEM, default), standard deviation (SD),
# or 95% confidence interval (CI) if using median
error_bars: SEM

# bandwidth of the fitted kernel density estimators. Determines smoothening of the
# stripes in each violin. "None" is the default value, which means an "optimal"
# factor will be calculated
bw: None

# whether the data is paired or not. Default is no.
paired_data: no

# overlay statistics on plot. Only works for 2 or 3 conditions.
stats_on_plot: yes

# minimum and maximum y values to display on the y-axis e.g. 1, 5. Default value: None
ylimits: None

# width of each violinplot. Default value: 0.8
total_width: 0.8

# width of the black lines around each violinplot and the skeleton plot. Default value: 1
linewidth: 1

# width of the black lines separating replicates in each violin. Default value: 0.5
sep_linewidth: 0.5

# whether to show a legend on the superviolin. The legend lists the names of the replicates
show_legend: no

# colours used for each individual replicates. List of potential colours available
# at https://matplotlib.org/stable/gallery/color/named_colors.html
# under the "CSS Colors" heading. Separate colours by ", " e.g. red, blue, green
# alternatively, use a colour map from
# https://matplotlib.org/stable/tutorials/colors/colormaps.html
cmap: Set2

# dpi used for rendering and saving Violin SuperPlots
dpi: 600
