QAQC Tissue Processing

NEFSC · Jan 8, 2025 · 594be40 · 594be40
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diff --git a/Lab_Data_TissueProcessing/code/LIS Oyster Lab Biometrics.Rmd b/Lab_Data_TissueProcessing/code/LIS Oyster Lab Biometrics.Rmd
@@ -5,9 +5,9 @@ Authot : Mariah Kachmar
 description: This R code is used to import and summarize tissue processing data (body condition, height/length/width, weight, sample collection) from the LISS Oyster Health Project's monthly sampling at Ash Creek and Fence Creek intertidal sites in Connecticut and Goldstar beach and Laurel Hollow subtidal sites on Long Island, NY. 
 ---
 
-Updated 12/11/24 by K. Lenderman
+Updated 1/08/25 by K. Lenderman
 - all code up to date & graphs generated
-
+- 2025 code added
 
 
 
@@ -179,7 +179,7 @@ mean_body_condition
   #filter(year == "2024")
 
 #Mean body condtion scores - 2023
-data_2023 <- data_all%>%  filter(!year=="2024")
+data_2023 <- data_all%>%  filter(year=="2023")
   
 ggplot(data=data_2023, aes(x=month, y=condition_score, group = month, fill = site)) +
   geom_boxplot()+ 
@@ -188,7 +188,7 @@ ggplot(data=data_2023, aes(x=month, y=condition_score, group = month, fill = sit
   labs(title="Mean Condition Score - 2023", x ="month", y = "Mean Body Condition Score")+ scale_y_reverse()+facet_wrap(~site)
 
 #Mean body condtion scores - 2024
-data_2024 <- data_all%>%  filter(!year=="2023")
+data_2024 <- data_all%>%  filter(year=="2024")
   
 ggplot(data=data_2024, aes(x=month, y=condition_score, group = month, fill = site)) +
   geom_boxplot()+ 
@@ -197,13 +197,13 @@ ggplot(data=data_2024, aes(x=month, y=condition_score, group = month, fill = sit
   labs(title="Mean Condition Score - 2024", x ="month", y = "Mean Body Condition Score")+ scale_y_reverse()+facet_wrap(~site)
 
 #Mean body condition scores - 2025
-#data_2025 <- data_all%>%  filter(year=="2025")
+data_2025 <- data_all%>%  filter(year=="2025")
   
-#ggplot(data=data_2025, aes(x=month, y=condition_score, group = month, fill = site)) +
-  #geom_boxplot()+ 
-  #theme_bw() +  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+ 
-  #theme(axis.text.x = element_text(angle = -35, vjust = 0.5, hjust=1))+
-  #labs(title="Mean Condition Score - 2025", x ="month", y = "Mean Body Condition Score")+ scale_y_reverse()+facet_wrap(~site)
+ggplot(data=data_2025, aes(x=month, y=condition_score, group = month, fill = site)) +
+  geom_boxplot()+ 
+  theme_bw() +  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+ 
+  theme(axis.text.x = element_text(angle = -35, vjust = 0.5, hjust=1))+
+  labs(title="Mean Condition Score - 2025", x ="month", y = "Mean Body Condition Score")+ scale_y_reverse()+facet_wrap(~site)
 ```
 #Proportions graph Body condition scores
 
@@ -290,8 +290,8 @@ print(BCS_proportion_all_2025)
 dev.off()
 ```
 ```{r}
-# Proportion per month of intensity scores at three sites during 2023 & 2024
-df_bcs_proportions_new <- rbind(df_BCS_proportions2023, df_BCS_proportions2024)
+# Proportion per month of intensity scores at three sites during 2023 & 2024 & 2025
+df_bcs_proportions_new <- rbind(df_BCS_proportions2023, df_BCS_proportions2024, df_BCS_proportions2025)
 
 df_bcs_proportions_new<- df_bcs_proportions_new %>% filter(!site=="LAUR")
 
@@ -389,15 +389,15 @@ print(ASHC_BCS_dist2024)
 dev.off()
 
 #Condition distribution across all sample months - 2025
-df_ASHC_2024 <- df_ASHC%>%  filter(year=="2025")
+df_ASHC_2025 <- df_ASHC%>%  filter(year=="2025")
 
 ASHC_BCS_dist2025 <-ggplot(data=df_ASHC_2025, aes(x= condition)) +
   geom_bar()+  #scale_fill_manual(values=c("forestgreen","orange", "purple"))+
   theme_bw() +  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+ 
   #theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
   labs(title="Ash Creek Body Condition Score - 2025", x ="Condition categorization")+
   facet_wrap(~ month, scales = "free")
-ASHC_BCS_dist2024
+ASHC_BCS_dist2025
 
 pdf(paste0(path = "Lab_Data_TissueProcessing/output" ,"/ASHC_BCS_dist_2025.pdf"), height = 7, width = 13)
 print(ASHC_BCS_dist2025)
@@ -456,7 +456,7 @@ ASHC_precent_greater_3 <- df_ASHC %>%
 ASHC_precent_greater_3
 
 ASHC_BCS_percentage <- ASHC_precent_greater_3%>% 
-  filter(year =="2024")%>%
+  #filter(year =="2024")%>%
   ggplot(aes(x = month, y = Percentage)) +
   #geom_bar(width = 0.5, stat = "identity", position = "fill") +
     geom_col()+

diff --git a/Lab_Data_TissueProcessing/code/LIS Oyster Lab Biometrics.nb.html b/Lab_Data_TissueProcessing/code/LIS Oyster Lab Biometrics.nb.html
diff --git a/Lab_Data_TissueProcessing/output/ASHC_BCS_dist_2023.pdf b/Lab_Data_TissueProcessing/output/ASHC_BCS_dist_2023.pdf
diff --git a/Lab_Data_TissueProcessing/output/ASHC_BCS_dist_2024.pdf b/Lab_Data_TissueProcessing/output/ASHC_BCS_dist_2024.pdf
diff --git a/Lab_Data_TissueProcessing/output/ASHC_BCS_dist_2025.pdf b/Lab_Data_TissueProcessing/output/ASHC_BCS_dist_2025.pdf
diff --git a/Lab_Data_TissueProcessing/output/ASHC_BCS_percentage.pdf b/Lab_Data_TissueProcessing/output/ASHC_BCS_percentage.pdf
diff --git a/Lab_Data_TissueProcessing/output/ASHC_BCS_proportion.pdf b/Lab_Data_TissueProcessing/output/ASHC_BCS_proportion.pdf
diff --git a/Lab_Data_TissueProcessing/output/Completeness_tissue_processing_data.csv b/Lab_Data_TissueProcessing/output/Completeness_tissue_processing_data.csv
@@ -17,6 +17,7 @@
 "ASHC",2024-10-21,30,109.723666666667,10.4333039311399,1.90485197079756,3.89585971455006,1
 "ASHC",2024-11-13,30,102.684,11.6946859726972,2.13514777006183,4.36686750966399,1
 "ASHC",2024-12-09,30,107.114,12.9817696046789,2.37013601627252,4.84747243636688,1
+"ASHC",2025-01-06,30,102.835,11.317903957889,2.06635710047094,4.22617479311455,1
 "FENC",2023-04-27,30,109.214,21.0432137639963,3.84194762031465,7.85766515658872,1
 "FENC",2023-05-15,30,126.406,15.7145102285798,2.8690639107796,5.86789455549962,1
 "FENC",2023-06-14,30,112.195666666667,16.2222009823773,2.96175513681017,6.05746939854297,1

diff --git a/Lab_Data_TissueProcessing/output/all_BCS_proportion_2024.pdf b/Lab_Data_TissueProcessing/output/all_BCS_proportion_2024.pdf
diff --git a/Lab_Data_TissueProcessing/output/all_BCS_proportion_2025.pdf b/Lab_Data_TissueProcessing/output/all_BCS_proportion_2025.pdf
diff --git a/Lab_Data_TissueProcessing/raw_data/Files_by_Month/0125ASHC_TissueProcessing - Master.csv b/Lab_Data_TissueProcessing/raw_data/Files_by_Month/0125ASHC_TissueProcessing - Master.csv
@@ -0,0 +1,37 @@
+lab_id,date_collected,site,lab_sample,date_processed,height_mm,condition,sample_notes,mantle_rftm,ggr1_frozen,ggr2_etoh,cross_histology,date_davidsons,date_etoh,,,
+0125ASHC_01,1/6/2025,ASHC,1,1/6/2025,93.24,5_fair,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_02,1/6/2025,ASHC,2,1/6/2025,97.88,4_fair_plus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_03,1/6/2025,ASHC,3,1/6/2025,100.32,4_fair_plus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_04,1/6/2025,ASHC,4,1/6/2025,112.22,6_fair_minus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_05,1/6/2025,ASHC,5,1/6/2025,98.98,5_fair,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_06,1/6/2025,ASHC,6,1/6/2025,93.9,6_fair_minus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_07,1/6/2025,ASHC,7,1/6/2025,115.85,3_good_minus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_08,1/6/2025,ASHC,8,1/6/2025,112.2,5_fair,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_09,1/6/2025,ASHC,9,1/6/2025,80.79,6_fair_minus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_10,1/6/2025,ASHC,10,1/6/2025,121.88,4_fair_plus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_11,1/6/2025,ASHC,11,1/6/2025,81.56,3_good_minus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_12,1/6/2025,ASHC,12,1/6/2025,100.9,3_good_minus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,  
+0125ASHC_13,1/6/2025,ASHC,13,1/6/2025,116.35,3_good_minus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_14,1/6/2025,ASHC,14,1/6/2025,97.59,3_good_minus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_15,1/6/2025,ASHC,15,1/6/2025,113.59,3_good_minus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_16,1/6/2025,ASHC,16,1/6/2025,90.13,3_good_minus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_17,1/6/2025,ASHC,17,1/6/2025,92.52,4_fair_plus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_18,1/6/2025,ASHC,18,1/6/2025,92.16,3_good_minus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_19,1/6/2025,ASHC,19,1/6/2025,109.4,4_fair_plus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_20,1/6/2025,ASHC,20,1/6/2025,125.16,3_good_minus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_21,1/6/2025,ASHC,21,1/6/2025,93.95,4_fair_plus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_22,1/6/2025,ASHC,22,1/6/2025,109.56,4_fair_plus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_23,1/6/2025,ASHC,23,1/6/2025,107.41,5_fair,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_24,1/6/2025,ASHC,24,1/6/2025,97.8,3_good_minus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_25,1/6/2025,ASHC,25,1/6/2025,102.37,4_fair_plus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_26,1/6/2025,ASHC,26,1/6/2025,104.64,4_fair_plus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_27,1/6/2025,ASHC,27,1/6/2025,119.11,4_fair_plus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_28,1/6/2025,ASHC,28,1/6/2025,107.46,5_fair,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_29,1/6/2025,ASHC,29,1/6/2025,91.28,4_fair_plus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+0125ASHC_30,1/6/2025,ASHC,30,1/6/2025,104.85,4_fair_plus,,TRUE,TRUE,TRUE,TRUE,1/6/2025,1/8/2025,,,
+,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,
+,,,,                                                                                                                     ,,,,,,,,,,,,
diff --git a/Lab_Data_TissueProcessing/raw_data/shell_pathology/0125ASHC_Pathology.csv b/Lab_Data_TissueProcessing/raw_data/shell_pathology/0125ASHC_Pathology.csv
@@ -0,0 +1,31 @@
+lab_id,pathology_notes,boring_sponge,shell_scarring,polydora,conchiolin_mod_severe,mud_blister,pea_crab,gill_erosion,pale_digestive,discoloration,horn_add,cyst_abscess,tumor
+0125ASHC_01,,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_02,,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE
+0125ASHC_03,,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE
+0125ASHC_04,,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE
+0125ASHC_05,,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_06,,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_07,,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_08,,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_09,,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_10,,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_11,,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_12,,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_13,,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_14,,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_15,,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE
+0125ASHC_16,,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_17,,FALSE,TRUE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_18,,FALSE,TRUE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_19,,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE
+0125ASHC_20,,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE
+0125ASHC_21,,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_22,,FALSE,TRUE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_23,,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_24,,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_25,Pink shell coloration above mantle,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_26,,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_27,,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_28,,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_29,,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
+0125ASHC_30,,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE