diff --git a/1_plot.R b/1_plot.R index 00eb8ad..10659db 100644 --- a/1_plot.R +++ b/1_plot.R @@ -30,7 +30,7 @@ p1_targets <- list( metab_data = p0_metab_timeseries_data, season_data = p0_season_cutoff_data, config = p0_config, - out_file = "1_plot/out/fig_6_metab_timeseries_plot.png" + out_file = "1_plot/out/fig_5_metab_timeseries_plot.tiff" ), format = "file" ), @@ -41,7 +41,7 @@ p1_targets <- list( load_data = p0_load_timeseries_data, inlake_data = p0_inlake_nutrient_timeseries_data, config = p0_config, - out_file = "1_plot/out/fig_S3_doc_timeseries_plot.png" + out_file = "1_plot/out/fig_S3_doc_timeseries_plot.tiff" ), format = "file" ), @@ -52,7 +52,7 @@ p1_targets <- list( load_data = p0_load_timeseries_data, inlake_data = p0_inlake_nutrient_timeseries_data, config = p0_config, - out_file = "1_plot/out/fig_S1_tp_timeseries_plot.png" + out_file = "1_plot/out/fig_S1_tp_timeseries_plot.tiff" ), format = "file" ), @@ -63,7 +63,7 @@ p1_targets <- list( load_data = p0_load_timeseries_data, inlake_data = p0_inlake_nutrient_timeseries_data, config = p0_config, - out_file = "1_plot/out/fig_S2_tn_timeseries_plot.png" + out_file = "1_plot/out/fig_S2_tn_timeseries_plot.tiff" ), format = "file" ), @@ -73,7 +73,7 @@ p1_targets <- list( load_data = p0_load_timeseries_data, inlake_data = p0_inlake_nutrient_timeseries_data, config = p0_config, - out_file = '1_plot/out/fig_4_stoich_timeseries_plot.png' + out_file = '1_plot/out/fig_S4_stoich_timeseries_plot.tiff' ), format = 'file' ), @@ -85,7 +85,7 @@ p1_targets <- list( inlake_data = p0_inlake_nutrient_timeseries_data, config = p0_config, label_id = p1_lake_label, - out_file = '1_plot/out/fig_2_stream_lake_nutrient_1_1.png' + out_file = '1_plot/out/fig_2_stream_lake_nutrient_1_1.tiff' ), format = 'file' ), @@ -97,7 +97,7 @@ p1_targets <- list( inlake_data = p0_inlake_nutrient_timeseries_data, config = p0_config, label_id = p1_lake_label, - out_file = '1_plot/out/fig_3_stream_lake_stoich_scatter.png' + out_file = '1_plot/out/fig_3_stream_lake_stoich_scatter.tiff' ), format = 'file' ), @@ -109,7 +109,7 @@ p1_targets <- list( inlake_data = p0_inlake_nutrient_timeseries_data, config = p0_config, label_id = p1_lake_label, - out_file = '1_plot/out/fig_5_plot_stoich_stream_vs_lake.png' + out_file = '1_plot/out/fig_4_plot_stoich_stream_vs_lake.tiff' ) ), @@ -118,7 +118,7 @@ p1_targets <- list( plot_obs_pred_metab_inlake( annual_data = p2_annual_data, label_id = p1_lake_label, - out_file = '1_plot/out/fig_S4_plot_obs_pred_metab_inlake.png' + out_file = '1_plot/out/fig_S5_plot_obs_pred_metab_inlake.tiff' ) ), @@ -127,7 +127,7 @@ p1_targets <- list( plot_obs_pred_metab_load( annual_data = p2_annual_data, label_id = p1_lake_label, - out_file = '1_plot/out/fig_S5_plot_obs_pred_metab_load.png' + out_file = '1_plot/out/fig_S6_plot_obs_pred_metab_load.tiff' ) ), @@ -160,7 +160,7 @@ p1_targets <- list( plot_models_inlake( annual_data = p2_annual_data, label_id = p1_lake_label, - out_file = '1_plot/out/fig_7_inlake_models.png' + out_file = '1_plot/out/fig_6_inlake_models.tiff' ) ), @@ -169,7 +169,7 @@ p1_targets <- list( plot_models_load( annual_data = p2_annual_data, label_id = p1_lake_label, - out_file = '1_plot/out/fig_8_load_models.png' + out_file = '1_plot/out/fig_7_load_models.tiff' ) ), @@ -178,7 +178,7 @@ p1_targets <- list( plot_doc_gpp( annual_data = p2_annual_data, label_id = p1_lake_label, - out_file = '1_plot/out/fig_S6_doc_gpp.png' + out_file = '1_plot/out/fig_S7_doc_gpp.tiff' ) ) ) diff --git a/1_plot/out/fig_2_stream_lake_nutrient_1_1.png b/1_plot/out/fig_2_stream_lake_nutrient_1_1.png deleted file mode 100644 index 46d2459..0000000 Binary files a/1_plot/out/fig_2_stream_lake_nutrient_1_1.png and /dev/null differ diff --git a/1_plot/out/fig_2_stream_lake_nutrient_1_1.tiff b/1_plot/out/fig_2_stream_lake_nutrient_1_1.tiff new file mode 100644 index 0000000..cb301ad Binary files /dev/null and b/1_plot/out/fig_2_stream_lake_nutrient_1_1.tiff differ diff --git a/1_plot/out/fig_3_stream_lake_stoich_scatter.png b/1_plot/out/fig_3_stream_lake_stoich_scatter.png deleted file mode 100644 index 10bebf6..0000000 Binary files a/1_plot/out/fig_3_stream_lake_stoich_scatter.png and /dev/null differ diff --git a/1_plot/out/fig_3_stream_lake_stoich_scatter.tiff b/1_plot/out/fig_3_stream_lake_stoich_scatter.tiff new file mode 100644 index 0000000..b64cbae Binary files /dev/null and b/1_plot/out/fig_3_stream_lake_stoich_scatter.tiff differ diff --git a/1_plot/out/fig_4_plot_stoich_stream_vs_lake.tiff b/1_plot/out/fig_4_plot_stoich_stream_vs_lake.tiff new file mode 100644 index 0000000..2fe73d0 Binary files /dev/null and b/1_plot/out/fig_4_plot_stoich_stream_vs_lake.tiff differ diff --git a/1_plot/out/fig_4_stoich_timeseries_plot.png b/1_plot/out/fig_4_stoich_timeseries_plot.png deleted file mode 100644 index 0348ddc..0000000 Binary files a/1_plot/out/fig_4_stoich_timeseries_plot.png and /dev/null differ diff --git a/1_plot/out/fig_5_metab_timeseries_plot.tiff b/1_plot/out/fig_5_metab_timeseries_plot.tiff new file mode 100644 index 0000000..0b3b5be Binary files /dev/null and b/1_plot/out/fig_5_metab_timeseries_plot.tiff differ diff --git a/1_plot/out/fig_5_plot_stoich_stream_vs_lake.png b/1_plot/out/fig_5_plot_stoich_stream_vs_lake.png deleted file mode 100644 index f7126ec..0000000 Binary files a/1_plot/out/fig_5_plot_stoich_stream_vs_lake.png and /dev/null differ diff --git a/1_plot/out/fig_6_inlake_models.tiff b/1_plot/out/fig_6_inlake_models.tiff new file mode 100644 index 0000000..7d6f501 Binary files /dev/null and b/1_plot/out/fig_6_inlake_models.tiff differ diff --git a/1_plot/out/fig_6_metab_timeseries_plot.png b/1_plot/out/fig_6_metab_timeseries_plot.png deleted file mode 100644 index c020ba3..0000000 Binary files a/1_plot/out/fig_6_metab_timeseries_plot.png and /dev/null differ diff --git a/1_plot/out/fig_7_inlake_models.png b/1_plot/out/fig_7_inlake_models.png deleted file mode 100644 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a/1_plot/out/fig_S2_tn_timeseries_plot.tiff b/1_plot/out/fig_S2_tn_timeseries_plot.tiff new file mode 100644 index 0000000..725b6b3 Binary files /dev/null and b/1_plot/out/fig_S2_tn_timeseries_plot.tiff differ diff --git a/1_plot/out/fig_S3_doc_timeseries_plot.png b/1_plot/out/fig_S3_doc_timeseries_plot.png deleted file mode 100644 index b4f767a..0000000 Binary files a/1_plot/out/fig_S3_doc_timeseries_plot.png and /dev/null differ diff --git a/1_plot/out/fig_S3_doc_timeseries_plot.tiff b/1_plot/out/fig_S3_doc_timeseries_plot.tiff new file mode 100644 index 0000000..b7f752e Binary files /dev/null and b/1_plot/out/fig_S3_doc_timeseries_plot.tiff differ diff --git a/1_plot/out/fig_S4_plot_obs_pred_metab_inlake.png b/1_plot/out/fig_S4_plot_obs_pred_metab_inlake.png deleted file mode 100644 index 5333382..0000000 Binary files a/1_plot/out/fig_S4_plot_obs_pred_metab_inlake.png and /dev/null differ diff --git a/1_plot/out/fig_S4_stoich_timeseries_plot.tiff b/1_plot/out/fig_S4_stoich_timeseries_plot.tiff new file mode 100644 index 0000000..dedcaa3 Binary files /dev/null and b/1_plot/out/fig_S4_stoich_timeseries_plot.tiff differ diff --git a/1_plot/out/fig_S5_plot_obs_pred_metab_inlake.tiff b/1_plot/out/fig_S5_plot_obs_pred_metab_inlake.tiff new file mode 100644 index 0000000..5f09c60 Binary files /dev/null and b/1_plot/out/fig_S5_plot_obs_pred_metab_inlake.tiff differ diff --git a/1_plot/out/fig_S5_plot_obs_pred_metab_load.png b/1_plot/out/fig_S5_plot_obs_pred_metab_load.png deleted file mode 100644 index 764ae2e..0000000 Binary files a/1_plot/out/fig_S5_plot_obs_pred_metab_load.png and /dev/null differ diff --git a/1_plot/out/fig_S6_doc_gpp.png b/1_plot/out/fig_S6_doc_gpp.png deleted file mode 100644 index f2d67d6..0000000 Binary files a/1_plot/out/fig_S6_doc_gpp.png and /dev/null differ diff --git a/1_plot/out/fig_S6_plot_obs_pred_metab_load.tiff b/1_plot/out/fig_S6_plot_obs_pred_metab_load.tiff new file mode 100644 index 0000000..994c8a5 Binary files /dev/null and b/1_plot/out/fig_S6_plot_obs_pred_metab_load.tiff differ diff --git a/1_plot/out/fig_S7_doc_gpp.tiff b/1_plot/out/fig_S7_doc_gpp.tiff new file mode 100644 index 0000000..33bce25 Binary files /dev/null and b/1_plot/out/fig_S7_doc_gpp.tiff differ diff --git a/1_plot/src/plotting_functions.R b/1_plot/src/plotting_functions.R index ea95b9b..bb548f9 100644 --- a/1_plot/src/plotting_functions.R +++ b/1_plot/src/plotting_functions.R @@ -71,7 +71,8 @@ plot_metab_timeseries <- function( ggsave(out_file, plot = metab, width = 10, - height = 10) + height = 10, + dpi = 400) } @@ -153,7 +154,8 @@ plot_doc_timeseries <- function( ggsave(out_file, plot = doc_load, - width = 10, height = 10) + width = 10, height = 10, + dpi = 400) } plot_tn_timeseries <- function( @@ -234,7 +236,8 @@ plot_tn_timeseries <- function( ggsave(out_file, plot = tn_load, - width = 10, height = 10) + width = 10, height = 10, + dpi = 400) } @@ -316,7 +319,8 @@ plot_tp_timeseries <- function( ggsave(out_file, plot = tp_load, - width = 10, height = 10) + width = 10, height = 10, + dpi = 400) } @@ -485,7 +489,8 @@ plot_stoich_timeseries <- function( ggsave(out_file, plot = lake_load_stoich, - width = 10, height = 10) + width = 10, height = 10, + dpi = 400) } @@ -627,7 +632,8 @@ plot_stream_lake_nutrient <- function( ggsave(out_file, plot = g, - width = 12, height = 4) + width = 12, height = 4, + dpi = 400) return(out_file) } @@ -992,7 +998,8 @@ plot_stream_lake_stoich_scatter <- function( browser() ggsave(out_file, plot = g, - width = 12, height = 8) + width = 12, height = 8, + dpi = 400) return(out_file) } @@ -1178,7 +1185,8 @@ plot_stoich_stream_vs_lake <- function( ggsave(out_file, plot = g, - width = 12, height = 4) + width = 12, height = 4, + dpi = 400) return(out_file) } @@ -1262,7 +1270,9 @@ plot_obs_pred_metab_inlake <- function( plot_out = cowplot::plot_grid(gpp, r, nep, nrow = 1) ggsave(filename = out_file, - plot = plot_out, width = 14, height =5 ) + plot = plot_out, + width = 14, height =5, + dpi = 400) return(out_file) } @@ -1449,7 +1459,9 @@ plot_obs_pred_metab_load <- function( plot_out = cowplot::plot_grid(gpp, r, nep, nrow = 1) ggsave(filename = out_file, - plot = plot_out, width = 14, height =5 ) + plot = plot_out, + width = 14, height =5, + dpi = 400) return(out_file) } @@ -1647,7 +1659,9 @@ plot_models_inlake <- function( "D", "E")) ggsave(filename = out_file, - plot = plot_out, width = 9, height = 14 ) + plot = plot_out, + width = 9, height = 14, + dpi = 350) return(out_file) } @@ -1816,7 +1830,9 @@ plot_models_load <- function( "G", "", "")) ggsave(filename = out_file, - plot = plot_out, width = 16, height = 16 ) + plot = plot_out, + width = 16, height = 16, + dpi = 300) return(out_file) } @@ -1872,7 +1888,9 @@ plot_doc_gpp <- function( ggrepel::geom_text_repel(aes(label=label_id)) ggsave(filename = out_file, - plot = gpp, width = 6, height = 6) + plot = gpp, + width = 6, height = 6, + dpi = 400) return(out_file) }