[inst/extdata/asalmon_mcw/main.r:2:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/inst/extdata/asalmon_mcw/main.r#L2) *style:* **Variable or function name should be snake_case.**
```r
LAMBDA_var <- 0.1 #Thin plate spline smoothing. Lambda=0 would be interpolation.
^~~~~~~~~~
```
[inst/extdata/asalmon_mcw/main.r:3:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/inst/extdata/asalmon_mcw/main.r#L3) *style:* **Variable or function name should be snake_case.**
```r
RESOLUTION_var <- 500 #Plot width in pixels
^~~~~~~~~~~~~~
```
[inst/extdata/asalmon_mcw/main.r:5:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/inst/extdata/asalmon_mcw/main.r#L5) *style:* **Lines should not be more than 80 characters.**
```r
#TODO change path. make sure this main.r script is just outside the diagram_retina folder.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/extdata/asalmon_mcw/main.r:8:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/inst/extdata/asalmon_mcw/main.r#L8) *style:* **Lines should not be more than 80 characters.**
```r
#todo verify these. see the tutorial here: https://github.com/bc/retina/blob/master/tutorial.md search for the part that starts with "#[V point of the tear,"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/extdata/asalmon_mcw/main.r:10:10:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/inst/extdata/asalmon_mcw/main.r#L10) *style:* **Commas should always have a space after.**
```r
    c(59,52,67),
         ^
```
[inst/extdata/asalmon_mcw/main.r:10:13:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/inst/extdata/asalmon_mcw/main.r#L10) *style:* **Commas should always have a space after.**
```r
    c(59,52,67),
            ^
```
[inst/extdata/asalmon_mcw/main.r:11:10:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/inst/extdata/asalmon_mcw/main.r#L11) *style:* **Commas should always have a space after.**
```r
    c(79,73,85),
         ^
```
[inst/extdata/asalmon_mcw/main.r:11:13:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/inst/extdata/asalmon_mcw/main.r#L11) *style:* **Commas should always have a space after.**
```r
    c(79,73,85),
            ^
```
[inst/extdata/asalmon_mcw/main.r:12:10:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/inst/extdata/asalmon_mcw/main.r#L12) *style:* **Commas should always have a space after.**
```r
    c(34,31,37))
         ^
```
[inst/extdata/asalmon_mcw/main.r:12:13:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/inst/extdata/asalmon_mcw/main.r#L12) *style:* **Commas should always have a space after.**
```r
    c(34,31,37))
            ^
```
[inst/extdata/asalmon_mcw/main.r:13:69:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/inst/extdata/asalmon_mcw/main.r#L13) *error:* **unexpected ')'**
```r
                                                                    )
                                                                    ^
```
[R/composite.R:2:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/composite.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
##' @description This is a subfunction, that is useful when creating average maps.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/composite.R:3:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/composite.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
##' @param retina_list A list containing retina objects, with names(retina_list) all defined.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/composite.R:4:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/composite.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
##' @param rotation_indices Each value in this vector will correspond to the amount of rotation applied to each retina in the list.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/composite.R:5:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/composite.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
##' @param ... Arguments passed from other functions. You can access the thin plate spline interpolator here.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/composite.R:6:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/composite.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
##' @return sum_mat The sum of all retina objects in the list, with respect to the rotation indices.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/composite.R:9:16:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/composite.R#L9) *warning:* **no visible global function definition for ‘mat_from_ret_obj’**
```r
    sum_mat <- mat_from_ret_obj(retina_list[[1]], rotation = 0, ...)
               ^~~~~~~~~~~~~~~~
```
[R/composite.R:12:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/composite.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
        sum_mat <- sum_mat + mat_from_ret_obj(retina_list[[i]], rotation_indices[i],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/composite.R:12:85:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/composite.R#L12) *style:* **Trailing whitespace is superfluous.**
```r
        sum_mat <- sum_mat + mat_from_ret_obj(retina_list[[i]], rotation_indices[i],
                                                                                ^
```
[R/matrix_retobj.R:3:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/matrix_retobj.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
##' You can decide how much to rotate the retina before returning the matrix. You can also pass arguments to the polar plotter.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/matrix_retobj.R:6:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/matrix_retobj.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
##' @param n the number by which to divide the matrix by. Useful when generating partial averages.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/matrix_retobj.R:7:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/matrix_retobj.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
##' @param reflect logical, by default it is TRUE, in order to view the retina from outside the eye (rather than from within.)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/matrix_retobj.R:12:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/matrix_retobj.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
mat_from_ret_obj <- function(retina_object, rotation = 0, n = 1, reflect = TRUE,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/matrix_retobj.R:12:81:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/matrix_retobj.R#L12) *style:* **Trailing whitespace is superfluous.**
```r
mat_from_ret_obj <- function(retina_object, rotation = 0, n = 1, reflect = TRUE,
                                                                                ^
```
[R/matrix_retobj.R:17:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/matrix_retobj.R#L17) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/matrix_retobj.R:20:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/matrix_retobj.R#L20) *style:* **Lines should not be more than 80 characters.**
```r
    az <- mapproject(x = retina_object$trimmed_data[, 2], retina_object$trimmed_data[,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/matrix_retobj.R:20:87:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/matrix_retobj.R#L20) *style:* **Trailing whitespace is superfluous.**
```r
    az <- mapproject(x = retina_object$trimmed_data[, 2], retina_object$trimmed_data[,
                                                                                ^
```
[R/matrix_retobj.R:25:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/matrix_retobj.R#L25) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/matrix_retobj.R:27:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/matrix_retobj.R#L27) *style:* **Lines should not be more than 80 characters.**
```r
    map2fit <- fit_plot_azimuthal(x2, y2, z2, plot_suppress = TRUE, extrapolate = TRUE,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/matrix_retobj.R:27:88:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/matrix_retobj.R#L27) *style:* **Trailing whitespace is superfluous.**
```r
    map2fit <- fit_plot_azimuthal(x2, y2, z2, plot_suppress = TRUE, extrapolate = TRUE,
                                                                                ^
```
[R/matrix_retobj.R:28:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/matrix_retobj.R#L28) *style:* **Lines should not be more than 80 characters.**
```r
        outer_radius = pi/2, falciform_coords = retina_object$azimuthal_data.falciform[[1]],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/matrix_retobj.R:28:26:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/matrix_retobj.R#L28) *style:* **Put spaces around all infix operators.**
```r
        outer_radius = pi/2, falciform_coords = retina_object$azimuthal_data.falciform[[1]],
                        ~^~
```
[R/matrix_retobj.R:28:93:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/matrix_retobj.R#L28) *style:* **Trailing whitespace is superfluous.**
```r
        outer_radius = pi/2, falciform_coords = retina_object$azimuthal_data.falciform[[1]],
                                                                                ^
```
[R/matrix_retobj.R:30:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/matrix_retobj.R#L30) *style:* **Variable or function name should be snake_case.**
```r
    MAT <- map2fit[[2]]$z
    ^~~
```
[R/matrix_retobj.R:32:15:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/matrix_retobj.R#L32) *style:* **Put spaces around all infix operators.**
```r
    return(MAT/n)
             ~^~
```
[R/plotting_functions.R:3:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
##' Extracts xy and falciform coordinates from datapoints collected from retistruct. Falc and Datapoints are stacked upon one another
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:5:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
##' @param datapoints_from_retistruct data structure that comes from the datapoints.csv, which is automatically generated by Retistruct.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:7:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
##' @return L list of pixel xy positions, and falciform coordinates in [1] and [2], respectively
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:9:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
extract_xy_and_falciform <- function(datapoints_from_retistruct, number_of_sampling_sites) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:10:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L10) *style:* **Lines should not be more than 80 characters.**
```r
    pixel_xy_positions <- datapoints_from_retistruct[1:number_of_sampling_sites,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:10:81:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L10) *style:* **Trailing whitespace is superfluous.**
```r
    pixel_xy_positions <- datapoints_from_retistruct[1:number_of_sampling_sites,
                                                                                ^
```
[R/plotting_functions.R:12:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
    falciform_len <- length(datapoints_from_retistruct[, 1]) - length(pixel_xy_positions[,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:12:91:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L12) *style:* **Trailing whitespace is superfluous.**
```r
    falciform_len <- length(datapoints_from_retistruct[, 1]) - length(pixel_xy_positions[,
                                                                                ^
```
[R/plotting_functions.R:16:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L16) *style:* **Lines should not be more than 80 characters.**
```r
    falciform_coordinates <- datapoints_from_retistruct[(xy_len + 1):total_len, ]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:22:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L22) *style:* **Lines should not be more than 80 characters.**
```r
##' ImageJ values don't always show up the right way, because Y values get larger and positive while moving down the image.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:24:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L24) *style:* **Lines should not be more than 80 characters.**
```r
##' @param falciform_xy_coordinates 2 columns of coordinate (X,Y) data in ImageJ pixel format
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:28:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L28) *style:* **Lines should not be more than 80 characters.**
```r
reflect_IJ_y_values_for_falciform <- function(falciform_xy_coordinates, xy_img_dimensions) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:28:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L28) *style:* **Variable and function names should not be longer than 30 characters.**
```r
reflect_IJ_y_values_for_falciform <- function(falciform_xy_coordinates, xy_img_dimensions) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:28:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L28) *style:* **Variable or function name should be snake_case.**
```r
reflect_IJ_y_values_for_falciform <- function(falciform_xy_coordinates, xy_img_dimensions) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:29:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L29) *style:* **Lines should not be more than 80 characters.**
```r
    falciform_xy_coordinates_transformed <- falciform_xy_coordinates  #make a copy
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:29:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L29) *style:* **Variable and function names should not be longer than 30 characters.**
```r
    falciform_xy_coordinates_transformed <- falciform_xy_coordinates  #make a copy
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:31:52:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L31) *style:* **Put spaces around all infix operators.**
```r
    half_of_vertical_pixels <- xy_img_dimensions[2]/2
                                                  ~^~
```
[R/plotting_functions.R:32:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L32) *style:* **Lines should not be more than 80 characters.**
```r
    falciform_xy_coordinates_transformed$cyan <- (falc_y - half_of_vertical_pixels) *
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:32:86:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L32) *style:* **Trailing whitespace is superfluous.**
```r
    falciform_xy_coordinates_transformed$cyan <- (falc_y - half_of_vertical_pixels) *
                                                                                ^
```
[R/plotting_functions.R:38:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L38) *style:* **Lines should not be more than 80 characters.**
```r
##' Shows a visualization of the outline, as well as the location of each datapoint, with fit plot.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:40:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L40) *style:* **Lines should not be more than 80 characters.**
```r
##' @param pixel_xy_positions 2 columns of coordinate (X,Y) data in ImageJ pixel format
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:41:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L41) *style:* **Lines should not be more than 80 characters.**
```r
##' @param z_vector numerical vector of density values for each of the coordinates
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:42:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L42) *style:* **Lines should not be more than 80 characters.**
```r
##' @param xy_outline_points 2 columns of coordinate(X,Y) data in ImageJ pixel format for the outline coordinates.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:45:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L45) *style:* **Lines should not be more than 80 characters.**
```r
traditional_flatmount_plot <- function(pixel_xy_positions, z_vector, xy_outline_points) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:46:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L46) *style:* **Lines should not be more than 80 characters.**
```r
    fit <- Tps(pixel_xy_positions, z_vector)  # fits a surface to ozone measurements.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:46:12:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L46) *warning:* **no visible global function definition for ‘Tps’, Did you mean 'Ops'?**
```r
    fit <- Tps(pixel_xy_positions, z_vector)  # fits a surface to ozone measurements.
           ^~~
```
[R/plotting_functions.R:47:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L47) *warning:* **no visible global function definition for ‘set.panel’**
```r
    set.panel(2, 2)
    ^~~~~~~~~
```
[R/plotting_functions.R:49:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L49) *warning:* **no visible global function definition for ‘set.panel’**
```r
    set.panel()
    ^~~~~~~~~
```
[R/plotting_functions.R:52:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L52) *warning:* **no visible global function definition for ‘surface’**
```r
    surface(fit)  # Quick image/contour plot of GCV surface.
    ^~~~~~~
```
[R/plotting_functions.R:61:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L61) *style:* **Lines should not be more than 80 characters.**
```r
##' Shows a visualization of the outline, as well as the location of each datapoint so the user can identify where the tears are.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:64:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L64) *style:* **Lines should not be more than 80 characters.**
```r
##' @param path_to_retina_data_folder The path to the folder that contains the outline.roi file.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:65:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L65) *style:* **Lines should not be more than 80 characters.**
```r
##' @return roi_coordinates XY vals of pixel coordinates of the outline points, in order.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:69:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L69) *style:* **Lines should not be more than 80 characters.**
```r
    roi_object <- read.ijroi(file.path(path_to_retina_data_folder, "outline.roi"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:69:19:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L69) *warning:* **no visible global function definition for ‘read.ijroi’**
```r
    roi_object <- read.ijroi(file.path(path_to_retina_data_folder, "outline.roi"))
                  ^~~~~~~~~~
```
[R/plotting_functions.R:70:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L70) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/plotting_functions.R:72:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L72) *style:* **Lines should not be more than 80 characters.**
```r
    # format plots has the coordinate (0, 0) in the top left.  We have the coordinate
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:73:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L73) *style:* **Lines should not be more than 80 characters.**
```r
    # (0, 0) in the bottom left. We need to transform P so that the outline appears
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:76:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L76) *style:* **Variable or function name should be snake_case.**
```r
    roi_XY_coords <- roi_object$coords
    ^~~~~~~~~~~~~
```
[R/plotting_functions.R:80:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L80) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/plotting_functions.R:81:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L81) *style:* **Lines should not be more than 80 characters.**
```r
    plot(roi_XY_coords, type = "l", col = "#d3d3d3", asp = 1, xlab = "X Pixels",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:81:81:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L81) *style:* **Trailing whitespace is superfluous.**
```r
    plot(roi_XY_coords, type = "l", col = "#d3d3d3", asp = 1, xlab = "X Pixels",
                                                                                ^
```
[R/plotting_functions.R:83:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L83) *style:* **Lines should not be more than 80 characters.**
```r
    text(roi_XY_coords[, 1], roi_XY_coords[, 2], labels = 1:length(roi_XY_coords[,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:83:83:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L83) *style:* **Trailing whitespace is superfluous.**
```r
    text(roi_XY_coords[, 1], roi_XY_coords[, 2], labels = 1:length(roi_XY_coords[,
                                                                                ^
```
[R/plotting_functions.R:85:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L85) *style:* **Lines should not be more than 80 characters.**
```r
    message("If you are getting this message, you are using a special feature. Contact me at brian.cohn@usc.edu and I will happily teach you how to use it.")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:93:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L93) *style:* **Lines should not be more than 80 characters.**
```r
##' @description Creates a markup.csv file. One of the dorsal_outline_index or nasal_outline_index must be filled in. Not both.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:96:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L96) *style:* **Lines should not be more than 80 characters.**
```r
##' @param dorsal_outline_index The index of the point that points toward dorsal, or NA.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:97:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L97) *style:* **Lines should not be more than 80 characters.**
```r
##' @param nasal_outline_index The index of the opint that points toward nasal, or NA.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:98:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L98) *style:* **Lines should not be more than 80 characters.**
```r
##' @param path_to_retina_data_folder The path where the markup.csv file will be saved.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:100:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L100) *style:* **Lines should not be more than 80 characters.**
```r
assemble_markup_file <- function(eye_left_or_right, path_to_retina_data_folder, dorsal_outline_index = NA,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:100:107:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L100) *style:* **Trailing whitespace is superfluous.**
```r
assemble_markup_file <- function(eye_left_or_right, path_to_retina_data_folder, dorsal_outline_index = NA,
                                                                                ^
```
[R/plotting_functions.R:104:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L104) *style:* **Lines should not be more than 80 characters.**
```r
        ## https://stackoverflow.com/questions/18509527/first-letter-to-upper-case
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:110:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L110) *style:* **Lines should not be more than 80 characters.**
```r
        line2 <- paste0("NA,", nasal_outline_index, ",0,NA,TRUE,\"", eye_side_string,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:110:86:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L110) *style:* **Trailing whitespace is superfluous.**
```r
        line2 <- paste0("NA,", nasal_outline_index, ",0,NA,TRUE,\"", eye_side_string,
                                                                                ^
```
[R/plotting_functions.R:113:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L113) *style:* **Lines should not be more than 80 characters.**
```r
        line2 <- paste0(dorsal_outline_index, ",NA", ",0,NA,TRUE,\"", eye_side_string,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:113:87:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L113) *style:* **Trailing whitespace is superfluous.**
```r
        line2 <- paste0(dorsal_outline_index, ",NA", ",0,NA,TRUE,\"", eye_side_string,
                                                                                ^
```
[R/plotting_functions.R:121:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L121) *style:* **Lines should not be more than 80 characters.**
```r
    message(paste("Wrote markup file to ", output_path, "\n Ensure that it exists beside your outline.roi file"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:131:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L131) *style:* **Lines should not be more than 80 characters.**
```r
##' @param tear_coordinates_dataframe the dataframe of 3 columns, with c('V0','VB','VF'), and n columns, where n= number of tears
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:132:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L132) *style:* **Lines should not be more than 80 characters.**
```r
##' @param path_to_retina_data_folder The path where the T.csv file will be saved.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:136:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L136) *style:* **Lines should not be more than 80 characters.**
```r
assemble_tear_file <- function(tear_coordinates_dataframe, path_to_retina_data_folder) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:139:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L139) *style:* **Lines should not be more than 80 characters.**
```r
    write.table(tear_coordinates_dataframe, output_path, sep = ",", row.names = FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:140:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L140) *style:* **Lines should not be more than 80 characters.**
```r
    message(paste("Wrote tear file to ", output_path, "\n Check that it exists beside your outline.roi file"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:148:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L148) *style:* **Lines should not be more than 80 characters.**
```r
##' @param path_to_retina_data_folder The path where the P.csv file will be saved.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:152:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L152) *style:* **Lines should not be more than 80 characters.**
```r
assemble_point_coordinates_file <- function(outline_coordinates, path_to_retina_data_folder) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:152:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L152) *style:* **Variable and function names should not be longer than 30 characters.**
```r
assemble_point_coordinates_file <- function(outline_coordinates, path_to_retina_data_folder) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:156:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L156) *style:* **Lines should not be more than 80 characters.**
```r
    message(paste("Wrote coordinates file to ", output_path, "\n Check that it exists beside your outline.roi file"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:178:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L178) *style:* **Variable and function names should not be longer than 30 characters.**
```r
plot_degree_label_for_latitudes <- function(outer_radius, circle.rads) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:178:59:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L178) *style:* **Variable or function name should be snake_case.**
```r
plot_degree_label_for_latitudes <- function(outer_radius, circle.rads) {
                                                          ^~~~~~~~~~~
```
[R/plotting_functions.R:179:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L179) *style:* **Lines should not be more than 80 characters.**
```r
    axis(2, pos = -1.25 * outer_radius, at = sort(union(circle.rads, -circle.rads)),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:179:85:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L179) *style:* **Trailing whitespace is superfluous.**
```r
    axis(2, pos = -1.25 * outer_radius, at = sort(union(circle.rads, -circle.rads)),
                                                                                ^
```
[R/plotting_functions.R:181:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L181) *style:* **Lines should not be more than 80 characters.**
```r
    text(-1.26 * outer_radius, sort(union(circle.rads, -circle.rads)), sort(union(circle.rads,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:181:95:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L181) *style:* **Trailing whitespace is superfluous.**
```r
    text(-1.26 * outer_radius, sort(union(circle.rads, -circle.rads)), sort(union(circle.rads,
                                                                                ^
```
[R/plotting_functions.R:196:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L196) *style:* **Lines should not be more than 80 characters.**
```r
    fields::image.plot(legend.only = TRUE, col = col, zlim = zlim, family = "Palatino")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:203:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L203) *style:* **Lines should not be more than 80 characters.**
```r
##' @param endpoints a 4 element numeric vector describing the xy and x'y' for the line segment.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:207:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L207) *style:* **Lines should not be more than 80 characters.**
```r
    segments(endpoints[1], endpoints[2], endpoints[3], endpoints[4], col = color_hex)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:217:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L217) *style:* **Lines should not be more than 80 characters.**
```r
##' @param endpoints vector of 4 numerics, x,y and x',y' defining the line segment
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:218:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L218) *style:* **Lines should not be more than 80 characters.**
```r
write_labels_at_endpoint_locations <- function(r_label, l_label, degree, endpoints) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:218:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L218) *style:* **Variable and function names should not be longer than 30 characters.**
```r
write_labels_at_endpoint_locations <- function(r_label, l_label, degree, endpoints) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:227:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L227) *style:* **Lines should not be more than 80 characters.**
```r
##' @description We do not need points plotted in the corners of the plotted circle.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:234:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L234) *style:* **Lines should not be more than 80 characters.**
```r
nullify_vals_outside_the_circle <- function(minitics, spatial_res, heatmap_matrix,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:234:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L234) *style:* **Variable and function names should not be longer than 30 characters.**
```r
nullify_vals_outside_the_circle <- function(minitics, spatial_res, heatmap_matrix,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:234:83:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L234) *style:* **Trailing whitespace is superfluous.**
```r
nullify_vals_outside_the_circle <- function(minitics, spatial_res, heatmap_matrix,
                                                                                ^
```
[R/plotting_functions.R:236:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L236) *style:* **Variable and function names should not be longer than 30 characters.**
```r
    matrix_position_is_within_the_circle <- function() {
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:239:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L239) *style:* **Variable or function name should be snake_case.**
```r
    markNA <- matrix(minitics, ncol = spatial_res, nrow = spatial_res)
    ^~~~~~
```
[R/plotting_functions.R:247:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L247) *style:* **Lines should not be more than 80 characters.**
```r
##' @description Find the location to put the label around the circle at each of the lines
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:252:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L252) *style:* **Variable and function names should not be longer than 30 characters.**
```r
compute_longitude_label_location <- function(axis.rads, outer_radius) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:252:46:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L252) *style:* **Variable or function name should be snake_case.**
```r
compute_longitude_label_location <- function(axis.rads, outer_radius) {
                                             ^~~~~~~~~
```
[R/plotting_functions.R:253:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L253) *style:* **Lines should not be more than 80 characters.**
```r
    return(c(RMat(axis.rads) %*% matrix(c(1.1, 0, -1.1, 0) * outer_radius, ncol = 2)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:253:14:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L253) *warning:* **no visible global function definition for ‘RMat’, Did you mean 'hat'?**
```r
    return(c(RMat(axis.rads) %*% matrix(c(1.1, 0, -1.1, 0) * outer_radius, ncol = 2)))
             ^~~~
```
[R/plotting_functions.R:262:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L262) *style:* **Lines should not be more than 80 characters.**
```r
    endpoints <- zapsmall(c(RMat(axis_radian) %*% matrix(c(1, 0, -1, 0) * outer_radius,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:262:88:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L262) *style:* **Trailing whitespace is superfluous.**
```r
    endpoints <- zapsmall(c(RMat(axis_radian) %*% matrix(c(1, 0, -1, 0) * outer_radius,
                                                                                ^
```
[R/plotting_functions.R:264:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L264) *warning:* **no visible global function definition for ‘draw_line_segments’**
```r
    draw_line_segments(endpoints)
    ^~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:268:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L268) *style:* **Lines should not be more than 80 characters.**
```r
##' @description put a degree label at the ends of the endpoints for each longitude
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:275:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L275) *style:* **Lines should not be more than 80 characters.**
```r
plot_longitudinal_labels <- function(axis.rad, outer_radius, r_label, l_label, degree) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:275:38:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L275) *style:* **Variable or function name should be snake_case.**
```r
plot_longitudinal_labels <- function(axis.rad, outer_radius, r_label, l_label, degree) {
                                     ^~~~~~~~
```
[R/plotting_functions.R:276:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L276) *style:* **Lines should not be more than 80 characters.**
```r
    write_labels_at_endpoint_locations(r_label, l_label, degree, compute_longitude_label_location(axis.rad,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:276:108:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L276) *style:* **Trailing whitespace is superfluous.**
```r
    write_labels_at_endpoint_locations(r_label, l_label, degree, compute_longitude_label_location(axis.rad,
                                                                                ^
```
[R/plotting_functions.R:286:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L286) *style:* **Variable or function name should be snake_case.**
```r
RMat <- function(radians) {
^~~~
```
[R/plotting_functions.R:287:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L287) *style:* **Lines should not be more than 80 characters.**
```r
    return(matrix(c(cos(radians), sin(radians), -sin(radians), cos(radians)), ncol = 2))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:291:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L291) *style:* **Lines should not be more than 80 characters.**
```r
##' @description plots radial lines, degree label for latitudes, and plots radial spokes with labels
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:296:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L296) *warning:* **no visible global function definition for ‘plot_circle_radial_lines’**
```r
    plot_circle_radial_lines(radius_vals)
    ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:297:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L297) *warning:* **no visible global function definition for ‘plot_degree_label_for_latitudes’**
```r
    plot_degree_label_for_latitudes(outer_radius, radius_vals)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:298:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L298) *warning:* **no visible global function definition for ‘plot_radial_spokes_and_labels’**
```r
    plot_radial_spokes_and_labels(outer_radius)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:325:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L325) *style:* **Variable and function names should not be longer than 30 characters.**
```r
define_color_breaks_based_on_source <- function(col_breaks_source, z, Mat) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:325:71:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L325) *style:* **Variable or function name should be snake_case.**
```r
define_color_breaks_based_on_source <- function(col_breaks_source, z, Mat) {
                                                                      ^~~
```
[R/plotting_functions.R:330:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L330) *style:* **Lines should not be more than 80 characters.**
```r
    } else if ((length(col_breaks_source) == 2) & (is.numeric(col_breaks_source))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:338:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L338) *style:* **Lines should not be more than 80 characters.**
```r
interpolate_input_data <- function(minitics, x, y, z, lambda, polynomial_m, extrapolate) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:339:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L339) *style:* **Lines should not be more than 80 characters.**
```r
    grid.list = list(x = minitics, y = minitics)  #choose locations to predict at
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:339:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L339) *style:* **Variable or function name should be snake_case.**
```r
    grid.list = list(x = minitics, y = minitics)  #choose locations to predict at
    ^~~~~~~~~
```
[R/plotting_functions.R:339:15:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L339) *style:* **Use <-, not =, for assignment.**
```r
    grid.list = list(x = minitics, y = minitics)  #choose locations to predict at
              ^
```
[R/plotting_functions.R:340:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L340) *style:* **Lines should not be more than 80 characters.**
```r
    t <- Tps(cbind(x, y), z, lambda = lambda, m = polynomial_m)  #computationally intensive
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:340:10:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L340) *warning:* **no visible global function definition for ‘Tps’, Did you mean 'Ops'?**
```r
    t <- Tps(cbind(x, y), z, lambda = lambda, m = polynomial_m)  #computationally intensive
         ^~~
```
[R/plotting_functions.R:341:12:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L341) *warning:* **no visible global function definition for ‘predictSurface’**
```r
    tmp <- predictSurface(t, grid.list, extrap = extrapolate)
           ^~~~~~~~~~~~~~
```
[R/plotting_functions.R:342:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L342) *style:* **Variable or function name should be snake_case.**
```r
    Mat <- tmp$z
    ^~~
```
[R/plotting_functions.R:354:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L354) *style:* **Variable or function name should be snake_case.**
```r
    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
    ^~~~~~~~~
```
[R/plotting_functions.R:354:25:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L354) *style:* **Put spaces around all infix operators.**
```r
    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
                       ~^~
```
[R/plotting_functions.R:354:31:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L354) *style:* **Put spaces around all infix operators.**
```r
    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
                             ~^~
```
[R/plotting_functions.R:354:37:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L354) *style:* **Put spaces around all infix operators.**
```r
    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
                                   ~^~
```
[R/plotting_functions.R:354:47:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L354) *style:* **Put spaces around all infix operators.**
```r
    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
                                             ~^~
```
[R/plotting_functions.R:354:57:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L354) *style:* **Put spaces around all infix operators.**
```r
    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
                                                       ~^~
```
[R/plotting_functions.R:355:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L355) *style:* **Variable or function name should be snake_case.**
```r
    r.labs <- c(90, 60, 30, 0, 330, 300)
    ^~~~~~
```
[R/plotting_functions.R:356:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L356) *style:* **Variable or function name should be snake_case.**
```r
    l.labs <- c(270, 240, 210, 180, 150, 120)
    ^~~~~~
```
[R/plotting_functions.R:358:9:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L358) *warning:* **no visible global function definition for ‘plot_longitudinal_lines’**
```r
        plot_longitudinal_lines(axis.rads[i], outer_radius)
        ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:359:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L359) *style:* **Lines should not be more than 80 characters.**
```r
        plot_longitudinal_labels(axis.rads[i], outer_radius, r.labs[i], l.labs[i],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:359:83:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L359) *style:* **Trailing whitespace is superfluous.**
```r
        plot_longitudinal_labels(axis.rads[i], outer_radius, r.labs[i], l.labs[i],
                                                                                ^
```
[R/plotting_functions.R:380:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L380) *style:* **Lines should not be more than 80 characters.**
```r
##' @description Useful for making the falciform process look more smooth and refined. This is purely aesthetic.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:381:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L381) *style:* **Lines should not be more than 80 characters.**
```r
##' @details enhance the resolution of a polygon vertices dataframe by creating a spline along each vertex.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:382:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L382) *style:* **Lines should not be more than 80 characters.**
```r
##' @param xy vertices in dataframe with x and y columns, in order (not all are used).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:389:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L389) *style:* **Lines should not be more than 80 characters.**
```r
##' @references http://gis.stackexchange.com/questions/24827/how-to-smooth-the-polygons-in-a-contour-map
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:398:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L398) *style:* **Variable or function name should be snake_case.**
```r
    data.spline <- spline(1:(n + 2 * k), data[, 1], n = vertices, ...)
    ^~~~~~~~~~~
```
[R/plotting_functions.R:402:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L402) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/plotting_functions.R:410:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L410) *style:* **Lines should not be more than 80 characters.**
```r
##' \code{retinaplot} Generates an Azimuthal Equidistant plot projection of a retina object.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:411:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L411) *style:* **Lines should not be more than 80 characters.**
```r
##' You can also set lambda(floating point number) and polynomial_m(integer), as well as extrapolate (TRUE, FALSE).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:412:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L412) *style:* **Lines should not be more than 80 characters.**
```r
##' @param inner_eye_view boolean, default is TRUE. If set to false, the plotted view of the retina will have the viewpoint within the skull looking at the rear of the eye. inner_eye_view has the same view as the traditional wholemount.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:415:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L415) *style:* **Lines should not be more than 80 characters.**
```r
##' @param return_fit logical, whether or not to return the interpolation fit data.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:417:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L417) *style:* **Lines should not be more than 80 characters.**
```r
##' @param retina_object A list containing an element \code{azimuthal_data.datapoints} with
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:418:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L418) *style:* **Lines should not be more than 80 characters.**
```r
##' \code{x,y,z} datapoints. File must also include \code{azimuthal_data.falciform}.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:426:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L426) *style:* **Lines should not be more than 80 characters.**
```r
retinaplot <- function(retina_object, spatial_res = 1000, rotation = 0, inner_eye_view = TRUE,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:426:95:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L426) *style:* **Trailing whitespace is superfluous.**
```r
retinaplot <- function(retina_object, spatial_res = 1000, rotation = 0, inner_eye_view = TRUE,
                                                                                ^
```
[R/plotting_functions.R:428:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L428) *style:* **Variable or function name should be snake_case.**
```r
    AZx <- retina_object$azimuthal_data.datapoints[[1]]$x
    ^~~
```
[R/plotting_functions.R:429:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L429) *style:* **Variable or function name should be snake_case.**
```r
    AZy <- retina_object$azimuthal_data.datapoints[[1]]$y
    ^~~
```
[R/plotting_functions.R:430:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L430) *style:* **Variable or function name should be snake_case.**
```r
    AZz <- retina_object$azimuthal_data.datapoints[[1]]$z
    ^~~
```
[R/plotting_functions.R:432:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L432) *style:* **Variable or function name should be snake_case.**
```r
    rotAZ <- cartesian_rotation(AZx, AZy, rotation)
    ^~~~~
```
[R/plotting_functions.R:432:14:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L432) *warning:* **no visible global function definition for ‘cartesian_rotation’**
```r
    rotAZ <- cartesian_rotation(AZx, AZy, rotation)
             ^~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:433:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L433) *style:* **Variable or function name should be snake_case.**
```r
    AZx <- rotAZ$x
    ^~~
```
[R/plotting_functions.R:434:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L434) *style:* **Variable or function name should be snake_case.**
```r
    AZy <- rotAZ$y
    ^~~
```
[R/plotting_functions.R:435:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L435) *style:* **Lines should not be more than 80 characters.**
```r
    rotFALC <- cartesian_rotation(retina_object$azimuthal_data.falciform[[1]]$x,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:435:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L435) *style:* **Variable or function name should be snake_case.**
```r
    rotFALC <- cartesian_rotation(retina_object$azimuthal_data.falciform[[1]]$x,
    ^~~~~~~
```
[R/plotting_functions.R:435:81:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L435) *style:* **Trailing whitespace is superfluous.**
```r
    rotFALC <- cartesian_rotation(retina_object$azimuthal_data.falciform[[1]]$x,
                                                                                ^
```
[R/plotting_functions.R:442:9:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L442) *style:* **Variable or function name should be snake_case.**
```r
        AZx <- AZx * -1
        ^~~
```
[R/plotting_functions.R:443:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L443) *style:* **Lines should not be more than 80 characters.**
```r
        retina_object$azimuthal_data.falciform[[1]]$x <- retina_object$azimuthal_data.falciform[[1]]$x *
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


他のメンバー様が企画関連二次創作をされた場合、情報を知りたいですか？
について
作られたメンバーの意向によって知らせたい場合は知りたいと思います。

と書きました。
今、メールを頂いて思いました。
誰が作ったとはなんとなく、とは思っていましたが本当にそうだとは思いませんでした。
また、
結論としては許可をとっています　とお知らせいただければ十分と感じました。

理由といたしましては、どうすればよいのかと考えていたことが時間の無駄に感じ、どっと疲れて不信感を持ったためです。
後からお知らせするかもしれない、というのはこういった意味でしたのですね。
理解不足でした。
申し訳ございませんが、次回からは　許可をとっている、だけお伝えいただけると助かります。
何度も書いて申し訳ございません。

この件でこちらの作業はおわりにします。