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corrredcell.Rmd
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corrredcell.Rmd
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# Correlation between redcell:total cells ratio VS total events/min
**Aim:** To see if the low number of redcells in some samples is influencing graph features These ratios are stored in "AKT1.redcell.ratio" "CTRL.redcell.ratio" "HRASV12.redcell.ratio" But I also need the events/min vars.. Need to see if there is correlation for ALL conditions, including AGE
example code to collect the vars:
```{r example code}
# Create a vector of variable names from different ranges
var_names <- c(
paste0("ID0", 130:132, "redcell.ratio"),
paste0("ID0", 139:143, "redcell.ratio")
)
# Use mget to retrieve values of these variables from the environment
values <- mget(var_names)
# Combine all values into HRASV12_5dpf.redcell.ratio
AKT1_5dpf.redcell.ratio <- unlist(values)
AKT1_5dpf.redcell.ratio
# For the frequency values:
all_AKT1_5dpf_freq <- c(
all_lists[["AKT1_5dpf_hind"]][grepl(pattern, names(all_lists[["AKT1_5dpf_hind"]]), perl = TRUE)],
all_lists[["AKT1_5dpf_mid"]][grepl(pattern, names(all_lists[["AKT1_5dpf_mid"]]), perl = TRUE)]
)
# order them so they parallel each other
# Sort AKT1_5dpf.redcell.ratio by the names
AKT1_5dpf.redcell.ratio <- AKT1_5dpf.redcell.ratio[order(names(AKT1_5dpf.redcell.ratio))]
# Sort all_AKT1_5dpf_freq by the names
all_AKT1_5dpf_freq <- all_AKT1_5dpf_freq[order(names(all_AKT1_5dpf_freq))]
```
Correlation analysis VS events/min (frequency):
```{r frequency}
correlation_result_CTRL_5dpf.freq <- cor.test(as.numeric(CTRL_4dpf.redcell.ratio), as.numeric(all_CTRL_4dpf_freq))
correlation_result_CTRL_5dpf.freq <- cor.test(as.numeric(CTRL_5dpf.redcell.ratio), as.numeric(all_CTRL_5dpf_freq))
correlation_result_HRASV12_4dpf.freq <- cor.test(as.numeric(HRASV12_4dpf.redcell.ratio), as.numeric(all_HRASV12_4dpf_freq))
correlation_result_HRASV12_5dpf.freq <- cor.test(as.numeric(HRASV12_5dpf.redcell.ratio), as.numeric(all_HRASV12_5dpf_freq))
correlation_result_AKT1_4dpf.freq <- cor.test(as.numeric(AKT1_4dpf.redcell.ratio), as.numeric(all_AKT1_4dpf_freq))
correlation_result_AKT1_5dpf.freq <- cor.test(as.numeric(AKT1_5dpf.redcell.ratio), as.numeric(all_AKT1_5dpf_freq))
# Print the correlation coefficient and p-value
print(paste0("CTRL 4dpf ", correlation_result_CTRL_4dpf.freq$p.value))
print(paste0("CTRL 5dpf ", correlation_result_CTRL_5dpf.freq$p.value))
print(paste0("HRASV12 4dpf ", correlation_result_HRASV12_4dpf.freq$p.value))
print(paste0("HRASV12 5dpf ", correlation_result_HRASV12_5dpf.freq$p.value))
print(paste0("AKT1 4dpf ", correlation_result_AKT1_4dpf.freq$p.value))
print(paste0("AKT1 4dpf ", correlation_result_AKT1_5dpf.freq$p.value))
```
Correlation analysis VS mean (deconvoluted) Calcium levels
```{r mean_Ca}
correlation_result_CTRL_4dpf.ca <- cor.test(as.numeric(CTRL_4dpf.redcell.ratio), as.numeric(CTRL_4dpf__mean_Ca))
correlation_result_CTRL_5dpf.ca <- cor.test(as.numeric(CTRL_5dpf.redcell.ratio), as.numeric(CTRL_5dpf__mean_Ca))
correlation_result_HRASV12_4dpf.ca <- cor.test(as.numeric(HRASV12_4dpf.redcell.ratio), as.numeric(HRASV12_4dpf__mean_Ca))
correlation_result_HRASV12_5dpf.ca <- cor.test(as.numeric(HRASV12_5dpf.redcell.ratio), as.numeric(HRASV12_5dpf__mean_Ca))
correlation_result_AKT1_4dpf.ca <- cor.test(as.numeric(AKT1_4dpf.redcell.ratio), as.numeric(AKT1_4dpf__mean_Ca))
correlation_result_AKT1_5dpf.ca <- cor.test(as.numeric(AKT1_5dpf.redcell.ratio), as.numeric(AKT1_5dpf__mean_Ca))
print(paste0("CTRL 4dpf ", correlation_result_CTRL_4dpf.ca$p.value))
print(paste0("CTRL 5dpf ", correlation_result_CTRL_5dpf.ca$p.value))
print(paste0("HRASV12 4dpf ", correlation_result_HRASV12_4dpf.ca$p.value))
print(paste0("HRASV12 5dpf ", correlation_result_HRASV12_5dpf.ca$p.value))
print(paste0("AKT1 4dpf ", correlation_result_AKT1_4dpf.ca$p.value))
print(paste0("AKT1 4dpf ", correlation_result_AKT1_5dpf.ca$p.value))
```
VS Global efficiency
```{r retrieving data}
# Updated pattern to exclude '.RFP' and capture only those with '_globalcoeff'
pattern <- "^(?!.*\\.RFP).*\\.globalcoeff$"
all_AKT1_4dpf_globaleff <- c(
all_lists[["AKT1_4dpf_hind"]][grepl(pattern, names(all_lists[["AKT1_4dpf_hind"]]), perl = TRUE)],
all_lists[["AKT1_4dpf_mid"]][grepl(pattern, names(all_lists[["AKT1_4dpf_mid"]]), perl = TRUE)]
)
# Order!
all_AKT1_4dpf_globaleff <- all_AKT1_4dpf_globaleff[order(names(all_AKT1_4dpf_globaleff))]
```
```{r total Global Efficiency}
correlation_result_CTRL_4dpf.globaleff <- cor.test(as.numeric(CTRL_4dpf.redcell.ratio), as.numeric(all_CTRL_4dpf_globaleff))
correlation_result_CTRL_5dpf.globaleff <- cor.test(as.numeric(CTRL_5dpf.redcell.ratio), as.numeric(all_CTRL_5dpf_globaleff))
correlation_result_HRASV12_4dpf.globaleff <- cor.test(as.numeric(HRASV12_4dpf.redcell.ratio), as.numeric(all_HRASV12_4dpf_globaleff))
correlation_result_HRASV12_5dpf.globaleff <- cor.test(as.numeric(HRASV12_5dpf.redcell.ratio), as.numeric(all_HRASV12_5dpf_globaleff))
correlation_result_AKT1_4dpf.globaleff <- cor.test(as.numeric(AKT1_4dpf.redcell.ratio), as.numeric(all_AKT1_4dpf_globaleff))
correlation_result_AKT1_5dpf.globaleff <- cor.test(as.numeric(AKT1_5dpf.redcell.ratio), as.numeric(all_AKT1_5dpf_globaleff))
print(paste0("CTRL 4dpf ", correlation_result_CTRL_4dpf.globaleff$p.value))
print(paste0("CTRL 5dpf ", correlation_result_CTRL_5dpf.globaleff$p.value))
print(paste0("HRASV12 4dpf ", correlation_result_HRASV12_4dpf.globaleff$p.value))
print(paste0("HRASV12 5dpf ", correlation_result_HRASV12_5dpf.globaleff$p.value))
print(paste0("AKT1 4dpf ", correlation_result_AKT1_4dpf.globaleff$p.value))
print(paste0("AKT1 4dpf ", correlation_result_AKT1_5dpf.globaleff$p.value))
```
VS Clustering Coefficient
```{r retrieve data}
pattern <- "^(?!.*\\.RFP).*\\.clustcoeff$"
all_AKT1_5dpf_clustcoeff <- c(
all_lists[["AKT1_5dpf_hind"]][grepl(pattern, names(all_lists[["AKT1_5dpf_hind"]]), perl = TRUE)],
all_lists[["AKT1_5dpf_mid"]][grepl(pattern, names(all_lists[["AKT1_5dpf_mid"]]), perl = TRUE)]
)
# Order!
all_AKT1_5dpf_clustcoeff <- all_AKT1_5dpf_clustcoeff[order(names(all_AKT1_5dpf_clustcoeff))]
```
```{r total Clustering Coefficient}
correlation_result_CTRL_4dpf.clustcoeff <- cor.test(as.numeric(CTRL_4dpf.redcell.ratio), as.numeric(all_CTRL_4dpf_clustcoeff))
correlation_result_CTRL_5dpf.clustcoeff <- cor.test(as.numeric(CTRL_5dpf.redcell.ratio), as.numeric(all_CTRL_5dpf_clustcoeff))
correlation_result_HRASV12_4dpf.clustcoeff <- cor.test(as.numeric(HRASV12_4dpf.redcell.ratio), as.numeric(all_HRASV12_4dpf_clustcoeff))
correlation_result_HRASV12_5dpf.clustcoeff <- cor.test(as.numeric(HRASV12_5dpf.redcell.ratio), as.numeric(all_HRASV12_5dpf_clustcoeff))
correlation_result_AKT1_4dpf.clustcoeff <- cor.test(as.numeric(AKT1_4dpf.redcell.ratio), as.numeric(all_AKT1_4dpf_clustcoeff))
correlation_result_AKT1_5dpf.clustcoeff <- cor.test(as.numeric(AKT1_5dpf.redcell.ratio), as.numeric(all_AKT1_5dpf_clustcoeff))
print(paste0("CTRL 4dpf ", correlation_result_CTRL_4dpf.clustcoeff$p.value))
print(paste0("CTRL 5dpf ", correlation_result_CTRL_5dpf.clustcoeff$p.value))
print(paste0("HRASV12 4dpf ", correlation_result_HRASV12_4dpf.clustcoeff$p.value))
print(paste0("HRASV12 5dpf ", correlation_result_HRASV12_5dpf.clustcoeff$p.value))
print(paste0("AKT1 4dpf ", correlation_result_AKT1_4dpf.clustcoeff$p.value))
print(paste0("AKT1 4dpf ", correlation_result_AKT1_5dpf.clustcoeff$p.value))
```