R/ExtractDB.R

In rubystokes/ECPT_Package:

ExtractDB <- function(x){
  tbl(SLAS2, "Per_Cell") %>%
    left_join(tbl(SLAS2, "Per_Image")) %>%
    select (Img_N = ImageNumber,
            Experiment = Image_Metadata_Experiment,
            Img_Nuclei_N = Image_Count_Nuclei,
            Cell_Type = Image_Metadata_Cell,
            Treatment = Image_Metadata_Treatment,
            Replicate = Image_Metadata_Replicate,
            Well = Image_Metadata_Well,
            Cell_N = Cell_Number_Object_Number,
            Cell_VEC_MeanI = Cell_Intensity_MeanIntensity_VECOrig) %>%
    collect() %>%
    cbind(tbl(SLAS2, "Cell_ActCl") %>%
            select (Cell_Act_Cl = class) %>%
            collect()) %>%
    cbind(tbl(SLAS2, "Per_CellJunctArea") %>%
            select (Junct_VEC_MeanI = CellJunctArea_Intensity_MeanIntensity_VECOrig) %>%
            collect()) %>%
    cbind(tbl(SLAS2, "Per_CellsObj") %>%
            select (Cell_NCheck = CellsObj_Number_Object_Number,
                    Cell_Area = CellsObj_AreaShape_Area,
                    Cell_Perim = CellsObj_AreaShape_Perimeter,
                    Cell_MaxL = CellsObj_AreaShape_MajorAxisLength,
                    Cell_MinL = CellsObj_AreaShape_MinorAxisLength,
                    Cell_Orientation = CellsObj_AreaShape_Orientation,
                    Cell_Neighbour_N = CellsObj_Neighbors_NumberOfNeighbors_Expanded,
                    Cell_1st_Nb_Dist = CellsObj_Neighbors_FirstClosestDistance_Expanded,
                    Cell_2nd_Nb_Dist = CellsObj_Neighbors_SecondClosestDistance_Expanded,
                    Perc_Touch = ) %>%
            collect()) %>%
    cbind(tbl(SLAS2, "Per_Nuclei") %>%
            select(Nu_X = Nuclei_Location_Center_X,
                   Nu_Y = Nuclei_Location_Center_Y,
                   DNA_IntI = Nuclei_Intensity_IntegratedIntensity_Nuclei,
                   Nu_Clustering = Nuclei_Neighbors_NumberOfNeighbors_20,
                   Nu_1st_Nb_Dist = Nuclei_Neighbors_FirstClosestDistance_20,
                   Nu_2nd_Nb_Dist = Nuclei_Neighbors_SecondClosestDistance_20,
                   Nu_Area = Nuclei_AreaShape_Area) %>%
            collect()) %>%
    cbind(tbl(SLAS2, "Per_NDotsCy") %>%
            select(Cy_NCH_IntI = NDotsCy_Intensity_IntegratedIntensity_NOTCH) %>%
            collect()) %>%
    cbind(tbl(SLAS2, "Per_NDotsNu") %>%
            select(Nu_NCH_IntI = NDotsNu_Intensity_IntegratedIntensity_NOTCH) %>%
            collect()) %>%
    cbind(tbl(SLAS2, "Per_CellsObj") %>%
            select (Stb_J_N = CellsObj_Children_Stb_Count,
                    Lin_J_N = CellsObj_Children_Lin_Count,
                    Jag_J_N = CellsObj_Children_Jag_Count,
                    NaJ_J_N = CellsObj_Children_NaJ_Count) %>%
            collect())
}