Add Proposal DM-20230302

experiments/Payload_Proposal_DM/20230302/20230302_IK.csv

@@ -0,0 +1,97 @@
+Plate,Well,ID,Type,Strain,Concentration,Area,Mean,Min,Max,Replicate,,,
+1-,A1,1-A1,Blank,YPD,0,10204,47.461,4,255,1,,,
+1-,A2,1-A2,Yeast,YHL033C,0,9922,46.579,3,255,1,,,
+1-,A3,1-A3,Yeast,YML058W,0,12875,67.821,6,255,1,,,
+1-,A4,1-A4,Yeast,YIL066C,0,10304,40.253,3,206,1,,,
+1-,A5,1-A5,Blank,Water,0,9248,30.68,1,210,1,,,
+1-,A6,1-A6,Dye,Fluorescein,0,9500,48.941,2,255,1,,,
+1-,A7,1-A7,Bacteria,G,0,9648,38.765,3,220,1,,,
+1-,A8,1-A8,Bacteria,M,0,10916,41.94,3,220,1,,,
+1-,A9,1-A9,Bacteria,C,0,4680,32.227,4,199,1,,,
+1-,A10,1-A10,Bacteria,I,0,9488,39.699,3,206,1,,,
+1-,A11,1-A11,Bacteria,K,0,10212,46.507,3,218,1,,,
+1-,A12,1-A12,Bacteria,E,0,7089,53.725,4,255,1,,,
+1-,B1,1-B1,Blank,YPD,0.15625,10204,35.481,2,224,1,,,
+1-,B2,1-B2,Yeast,YHL033C,0.15625,11125,41.916,4,215,1,,,
+1-,B3,1-B3,Yeast,YML058W,0.15625,11208,47.486,6,255,1,,,
+1-,B4,1-B4,Yeast,YIL066C,0.15625,10304,32.15,2,200,1,,,
+1-,B5,1-B5,Blank,Water,0.15625,8492,26.276,1,207,1,,,
+1-,B6,1-B6,Dye,Fluorescein,0.15625,10302,43.062,3,255,1,,,
+1-,B7,1-B7,Bacteria,G,0.15625,10005,34.562,3,253,1,,,
+1-,B8,1-B8,Bacteria,M,0.15625,9681,30.605,1,245,1,,,
+1-,B9,1-B9,Bacteria,C,0.15625,8329,40.24,4,255,1,,,
+1-,B10,1-B10,Bacteria,I,0.15625,9488,31.555,3,201,1,,,
+1-,B11,1-B11,Bacteria,K,0.15625,10753,41.126,3,247,1,,,
+1-,B12,1-B12,Bacteria,E,0.15625,7089,41.525,4,216,1,,,
+1-,C1,1-C1,Blank,YPD,0.3125,8820,50.081,8,255,1,,,
+1-,C2,1-C2,Yeast,YHL033C,0.3125,10302,48.036,6,255,1,,,
+1-,C3,1-C3,Yeast,YML058W,0.3125,11046,64.155,7,25,1,,,
+1-,C4,1-C4,Yeast,YIL066C,0.3125,12382,54.86,9,255,1,,,
+1-,C5,1-C5,Blank,Water,0.3125,12382,52.279,3,255,1,,,
+1-,C6,1-C6,Dye,Fluorescein,0.3125,12382,70.916,14,255,1,,,
+1-,C7,1-C7,Bacteria,G,0.3125,11208,41.68,5,255,1,,,
+1-,C8,1-C8,Bacteria,M,0.3125,13364,49.159,3,255,1,,,
+1-,C9,1-C9,Bacteria,C,0.3125,10486,49.079,6,255,1,,,
+1-,C10,1-C10,Bacteria,I,0.3125,10106,43.586,6,255,1,,,
+1-,C11,1-C11,Bacteria,K,0.3125,10753,46.205,5,255,1,,,
+1-,C12,1-C12,Bacteria,E,0.3125,10753,54.847,4,220,1,,,
+1-,D1,1-D1,Blank,YPD,0.625,10400,38.446,4,236,1,,,
+1-,D2,1-D2,Yeast,YHL033C,0.625,12168,44.545,9,198,1,,,
+1-,D3,1-D3,Yeast,YML058W,0.625,12475,56.8,7,255,1,,,
+1-,D4,1-D4,Yeast,YIL066C,0.625,12382,47.097,6,199,1,,,
+1-,D5,1-D5,Blank,Water,0.625,12380,48.657,1,226,1,,,
+1-,D6,1-D6,Dye,Fluorescein,0.625,14638,85.588,17,255,1,,,
+1-,D7,1-D7,Bacteria,G,0.625,12064,39.377,3,201,1,,,
+1-,D8,1-D8,Bacteria,M,0.625,13170,48.337,5,223,1,,,
+1-,D9,1-D9,Bacteria,C,0.625,13170,54.722,7,255,1,,,
+1-,D10,1-D10,Bacteria,I,0.625,12452,38.19,5,197,1,,,
+1-,D11,1-D11,Bacteria,K,0.625,13996,48.225,6,196,1,,,
+1-,D12,1-D12,Bacteria,E,0.625,13996,55.457,5,255,1,,,
+1-,E1,1-E1,Blank,LB_Cam,1.25,10944,42.465,2,255,1,,,
+1-,E2,1-E2,Yeast,YHL033C,1.25,13048,56.156,5,200,1,,,
+1-,E3,1-E3,Yeast,YML058W,1.25,12544,66.419,7,247,1,,,
+1-,E4,1-E4,Yeast,YIL066C,1.25,12168,30.245,6,98,1,,,
+1-,E5,1-E5,Blank,Water,1.25,11869,37.038,2,216,1,,,
+1-,E6,1-E6,Dye,Fluorescein,1.25,12980,91.153,30,243,1,,,
+1-,E7,1-E7,Bacteria,G,1.25,10106,45.325,7,205,1,,,
+1-,E8,1-E8,Bacteria,M,1.25,10752,47.869,6,206,1,,,
+1-,E9,1-E9,Bacteria,C,1.25,11782,68.41,15,255,1,,,
+1-,E10,1-E10,Bacteria,I,1.25,13996,43.345,8,217,1,,,
+1-,E11,1-E11,Bacteria,K,1.25,12942,44.121,7,200,1,,,
+1-,E12,1-E12,Bacteria,E,1.25,11598,64.334,10,255,1,,,
+1-,F1,1-F1,Blank,LB_Cam,2.5,10207,71.754,13,255,1,,,
+1-,F2,1-F2,Yeast,YHL033C,2.5,14432,92.737,20,213,1,,,
+1-,F3,1-F3,Yeast,YML058W,2.5,14432,104.098,43,207,1,,,
+1-,F4,1-F4,Yeast,YIL066C,2.5,13598,70.878,22,199,1,,,
+1-,F5,1-F5,Blank,Water,2.5,11516,58.258,3,255,1,,,
+1-,F6,1-F6,Dye,Fluorescein,2.5,15172,168.146,110,255,1,,,
+1-,F7,1-F7,Bacteria,G,2.5,13699,55.209,10,228,1,,,
+1-,F8,1-F8,Bacteria,M,2.5,15080,63.322,10,224,1,,,
+1-,F9,1-F9,Bacteria,C,2.5,15080,76.321,15,240,1,,,
+1-,F10,1-F10,Bacteria,I,2.5,13994,67.24,17,239,1,,,
+1-,F11,1-F11,Bacteria,K,2.5,15300,65.47,12,208,1,,,
+1-,F12,1-F12,Bacteria,E,2.5,15300,76.036,12,201,1,,,
+1-,G1,1-G1,Blank,LB_Cam,5,11703,56.331,5,202,1,,,
+1-,G2,1-G2,Yeast,YHL033C,5,15946,86.542,31,189,1,,,
+1-,G3,1-G3,Yeast,YML058W,5,15502,96.171,33,193,1,,,
+1-,G4,1-G4,Yeast,YIL066C,5,15172,57.862,21,177,1,,,
+1-,G5,1-G5,Blank,Water,5,15172,53.698,4,224,1,,,
+1-,G6,1-G6,Dye,Fluorescein,5,15076,186.076,125,255,1,,,
+1-,G7,1-G7,Bacteria,G,5,15080,57.47,12,192,1,,,
+1-,G8,1-G8,Bacteria,M,5,16168,62.683,18,185,1,,,
+1-,G9,1-G9,Bacteria,C,5,16168,99.574,13,194,1,,,
+1-,G10,1-G10,Bacteria,I,5,15300,77.381,28,189,1,,,
+1-,G11,1-G11,Bacteria,K,5,15510,64.916,19,194,1,,,
+1-,G12,1-G12,Bacteria,E,5,15510,83.625,23,234,1,,,
+1-,H1,1-H1,Blank,LB_Cam,10,8305,57.21,9,243,1,,,
+1-,H2,1-H2,Yeast,YHL033C,10,13260,84.419,41,148,1,,,
+1-,H3,1-H3,Yeast,YML058W,10,12546,113.821,79,255,1,,,
+1-,H4,1-H4,Yeast,YIL066C,10,13188,41.962,15,86,1,,,
+1-,H5,1-H5,Blank,Water,10,11272,39.392,4,219,1,,,
+1-,H6,1-H6,Dye,Fluorescein,10,13892,197.685,93,255,1,,,
+1-,H7,1-H7,Bacteria,G,10,9968,66.947,24,170,1,,,
+1-,H8,1-H8,Bacteria,M,10,13796,76.293,25,192,1,,,
+1-,H9,1-H9,Bacteria,C,10,13699,155.473,76,210,1,,,
+1-,H10,1-H10,Bacteria,I,10,13786,108.07,49,202,1,,,
+1-,H11,1-H11,Bacteria,K,10,14206,78.126,27,152,1,,,
+1-,H12,1-H12,Bacteria,E,10,13364,96.419,32,212,1,,,

experiments/Payload_Proposal_DM/20230302/plotting.R

@@ -0,0 +1,60 @@
+# Load libraries
+library(dplyr)
+library(tidyverse)
+library(ggplot2)
+library(RColorBrewer)
+library(wesanderson)
+
+# Set paths
+data_path <-
+data_filename <- "20230302_IK"
+
+# Set wd
+setwd(data_path)
+
+# Load data
+data <- read.csv(file.path(data_path, file.path(data_filename, "csv", fsep = ".")), header = TRUE, stringsAsFactors = FALSE)
+
+# Exclude wells with just media or water
+data_plot <- subset(data, Type != "Blank")
+
+# Select wells with just media or water
+# data_plot <- subset(data, Type == "Blank")
+
+# Rename values
+data_plot[data_plot == "I"] <- "E. coli (J23100)"
+data_plot[data_plot == "K"] <- "E. coli (J23104)"
+data_plot[data_plot == "C"] <- "E. coli (J23101)"
+data_plot[data_plot == "E"] <- "E. coli (J23106)"
+data_plot[data_plot == "M"] <- "E. coli (J23116)"
+data_plot[data_plot == "G"] <- "E. coli (J23117)"
+
+data_plot[data_plot == "YHL033C"] <- "Yeast (YHL033C)"
+data_plot[data_plot == "YIL066C"] <- "Yeast (YIL066C)"
+data_plot[data_plot == "YML058W"] <- "Yeast (YML058W)"
+
+# Order strains (E. coli plasmids by expression strength)
+# data_plot$Strain <- factor(data_plot$Strain, levels = c("Fluorescein", "YHL033C", "YIL066C", "YML058W", "I", "K", "C", "E", "M", "G"))
+
+data_plot$Strain <- factor(data_plot$Strain, levels = c("Fluorescein", "Yeast (YHL033C)", "Yeast (YIL066C)", "Yeast (YML058W)", "E. coli (J23100)", "E. coli (J23104)", "E. coli (J23101)", "E. coli (J23106)", "E. coli (J23116)", "E. coli (J23117)"))
+
+
+# Choose color palettes
+gp1 <- wes_palettes$Darjeeling1
+gp2 <- wes_palettes$Darjeeling2
+
+# Plotting
+ggplot(data_plot, aes(x = as.factor(Concentration), y = as.numeric(Mean)))+
+    geom_point(color = "#87c487", size = 6) +
+    # geom_smooth() +
+    theme_bw(base_size = 25) +
+    # geom_errorbar(aes(ymin=Mean-sd, ymax=Mean+sd), width=.2,
+    # position=position_dodge(.01)) +  
+    labs(x = "Concentration factor", y = "Brightness (a.u.)") +
+    theme(strip.text = element_text(face = "bold", hjust = 0, size = 20),
+        strip.background = element_rect(fill = "#FFFFFF"),
+        axis.text.x = element_text(angle=60, hjust=1)) +
+    facet_wrap(~Strain)
+    # facet_grid(cols = vars(Strain), rows = vars(Type))
+
+ggsave("20230302_IK.pdf")