Updates to zebreg

DillanSaunders · Jun 14, 2021 · 0194f9b · 0194f9b
1 parent 69eab48
commit 0194f9b
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Showing 39 changed files with 14 additions and 5 deletions.
diff --git a/comparing_distributions.Rmd b/comparing_distributions.Rmd
@@ -29,16 +29,18 @@ gg_qq_empirical <- function(original , imputed , gene, color, quantiles = seq(0,
     labs(x = paste(gene, "(Original)"),
          y= paste(gene, "(Imputed)"))
 }
+
+
 base_family = "Trebuchet MS"
-base_size = 40
+base_size = 60
 ```
 
 ```{r importing combined csv}
 imputed_18ss <- read.csv("./datasets/merged_csv/18ss_combined.csv")
 
 stt_posterior <- read.csv("./datasets/merged_csv/stt_posterior.csv")
 colnames(stt_posterior)[1] <- "sample_no"
-
+stt_posterior
 sthc_posterior <- read.csv("./datasets/merged_csv/sthc_posterior.csv")
 colnames(sthc_posterior)[1] <- "sample_no"
 
@@ -222,7 +224,7 @@ imputed_18ss_id3<- imputed_18ss %>%
 ```
 
 ```{r qqplot}
-
+base_size = 30
 qq_tbxta <- gg_qq_empirical((tbxta_18ss), imputed_18ss_tbxta, "tbxta", "brown3")
 qq_tbxta <- qq_tbxta + theme_bw(base_family = base_family, base_size = base_size) + coord_equal()
 qq_tbxta
@@ -270,13 +272,13 @@ ggsave("./results/qqplots/qq_znf703.png", qq_znf703)
 
 qq_depdc7a <- gg_qq_empirical((depdc7a_18ss), imputed_18ss_depdc7a, "depdc7a", "blueviolet")
 qq_depdc7a <- qq_depdc7a + theme_bw(base_family = base_family, base_size = base_size) + coord_equal()
-
+qq_depdc7a
 ggsave("./results/qqplots/qq_depdc7a.png", qq_depdc7a)
 
 
 qq_tagln3b <- gg_qq_empirical((tagln3b_18ss), imputed_18ss_tagln3b, "tagln3b", "coral")
 qq_tagln3b <- qq_tagln3b + theme_bw(base_family = base_family, base_size = base_size) + coord_equal()
-
+qq_tagln3b
 ggsave("./results/qqplots/qq_tagln3b.png", qq_tagln3b)
 
 

diff --git a/results/composite map/18ss/SUM_18ss_sthc_cdh6_imputed (2).png b/results/composite map/18ss/SUM_18ss_sthc_cdh6_imputed (2).png
diff --git a/results/composite map/18ss/SUM_sthc_hes6_imputed (1).png b/results/composite map/18ss/SUM_sthc_hes6_imputed (1).png
diff --git a/results/composite map/18ss/SUM_stsc_sp5l_imputed (2).png b/results/composite map/18ss/SUM_stsc_sp5l_imputed (2).png
diff --git a/results/composite map/18ss/SUM_stt_sox2_imputed (4).png b/results/composite map/18ss/SUM_stt_sox2_imputed (4).png
diff --git a/results/composite map/18ss/SUM_stt_tbxta_imputed.png b/results/composite map/18ss/SUM_stt_tbxta_imputed.png
diff --git a/results/composite map/18ss/SUM_stt_tcf_imputed (1).png b/results/composite map/18ss/SUM_stt_tcf_imputed (1).png
diff --git a/results/composite map/18ss/SUM_sttc_tagln3b_imputed (2).png b/results/composite map/18ss/SUM_sttc_tagln3b_imputed (2).png
diff --git a/results/composite map/18ss/SUM_sttc_tagln3b_original (1).png b/results/composite map/18ss/SUM_sttc_tagln3b_original (1).png
diff --git a/results/composite map/18ss/SUM_stzc_znf703_imputed.png b/results/composite map/18ss/SUM_stzc_znf703_imputed.png
diff --git a/results/composite map/24ss/SUM_24ss_sthc_hes6_imputed.png b/results/composite map/24ss/SUM_24ss_sthc_hes6_imputed.png
diff --git a/results/composite map/24ss/SUM_24ss_sthc_tagln3b_imputed.png b/results/composite map/24ss/SUM_24ss_sthc_tagln3b_imputed.png
diff --git a/results/composite map/24ss/SUM_24ss_sthc_tbxta_imputed.png b/results/composite map/24ss/SUM_24ss_sthc_tbxta_imputed.png
diff --git a/results/composite map/24ss/SUM_24ss_stsc_cdh6_imputed (1).png b/results/composite map/24ss/SUM_24ss_stsc_cdh6_imputed (1).png
diff --git a/results/composite map/24ss/SUM_24ss_stsc_sox2_imputed (1).png b/results/composite map/24ss/SUM_24ss_stsc_sox2_imputed (1).png
diff --git a/results/composite map/24ss/SUM_24ss_stsc_sp5l_imputed.png b/results/composite map/24ss/SUM_24ss_stsc_sp5l_imputed.png
diff --git a/results/composite map/24ss/SUM_24ss_stt_tcf_imputed (2).png b/results/composite map/24ss/SUM_24ss_stt_tcf_imputed (2).png
diff --git a/results/composite map/24ss/SUM_24ss_stzc_znf703_imputed.png b/results/composite map/24ss/SUM_24ss_stzc_znf703_imputed.png
diff --git a/results/composite map/28ss/SUM_28ss_sthc_hes6_imputed.png b/results/composite map/28ss/SUM_28ss_sthc_hes6_imputed.png
diff --git a/results/composite map/28ss/SUM_28ss_stsc_sp5l_imputed.png b/results/composite map/28ss/SUM_28ss_stsc_sp5l_imputed.png
diff --git a/results/composite map/28ss/SUM_28ss_stt_tcf_imputed.png b/results/composite map/28ss/SUM_28ss_stt_tcf_imputed.png
diff --git a/results/composite map/28ss/SUM_28ss_sttc_tagln3b_imputed.png b/results/composite map/28ss/SUM_28ss_sttc_tagln3b_imputed.png
diff --git a/results/composite map/28ss/SUM_28ss_stzc_cdh6_imputed.png b/results/composite map/28ss/SUM_28ss_stzc_cdh6_imputed.png
diff --git a/results/composite map/28ss/SUM_28ss_stzc_sox2_imputed.png b/results/composite map/28ss/SUM_28ss_stzc_sox2_imputed.png
diff --git a/results/composite map/28ss/SUM_28ss_stzc_tbxta_imputed.png b/results/composite map/28ss/SUM_28ss_stzc_tbxta_imputed.png
diff --git a/results/composite map/28ss/SUM_28ss_stzc_znf703_imputed.png b/results/composite map/28ss/SUM_28ss_stzc_znf703_imputed.png
diff --git a/results/composite map/Macro.ijm.ijm.ijm b/results/composite map/Macro.ijm.ijm.ijm
@@ -0,0 +1,7 @@
+run("Z Project...", "projection=[Sum Slices]");
+run("Subtract Background...", "rolling=3 light create sliding");
+run("mpl-magma");
+//run("Brightness/Contrast...");
+resetMinAndMax();
+run("Enhance Contrast", "saturated=0.35");
+
diff --git a/results/images/imputed/SUM_24ss_stt_tbxta_imputed.tif b/results/images/imputed/SUM_24ss_stt_tbxta_imputed.tif
diff --git a/results/images/imputed/SUM_24ss_stt_tcf_imputed.png b/results/images/imputed/SUM_24ss_stt_tcf_imputed.png
diff --git a/results/images/imputed/bgroll_SUM_24ss_stt_tcf_imputed.png b/results/images/imputed/bgroll_SUM_24ss_stt_tcf_imputed.png
diff --git a/results/images/original/SUM_24ss_tbxta_original.png b/results/images/original/SUM_24ss_tbxta_original.png
diff --git a/results/images/original/SUM_24ss_tcf_original.png b/results/images/original/SUM_24ss_tcf_original.png
diff --git a/results/images/original/bgroll_SUM_24ss_tcf_original.png b/results/images/original/bgroll_SUM_24ss_tcf_original.png
diff --git a/results/plots/fitness.png b/results/plots/fitness.png
diff --git a/results/plots/mae.png b/results/plots/mae.png
diff --git a/results/plots/rmse.png b/results/plots/rmse.png
diff --git a/results/qqplots/qq_sox2.png b/results/qqplots/qq_sox2.png
diff --git a/results/qqplots/qq_sp5l.png b/results/qqplots/qq_sp5l.png
diff --git a/results/qqplots/qq_tbxta.png b/results/qqplots/qq_tbxta.png