In vincent-van-hoef/Analysis5204: Analysis for NBIS support project #5204

Correlation

To assess how each protein's expression follows with two inflammation markers and the Birmingham Vasculitis Activity Score, correlation coefficients were calculated. In particular, Pearson correlations of each protein versus crp, sr and bvas values were calculated.

Plasma

crp

The full list of protein-wise Pearson correlation results for the different phenotypes with crp is collected in excel files in Results/Plasma/Correlation/crp/crp_phenotype_pearson_correlation.xlsx and shown in the table below.

All individuals regressions are plotted and collected in the subfolder regression_plots/ (see Figure \@ref(fig:crpCorr)). MPA and GPA or MPO and PR3 are each plotted on the same plot, but visualized in a different color.

knitr::include_graphics(c("Results/Plasma/Correlation/crp/regression_plots/CCL18_PARC_GPA_MPA_regression.pdf", "Results/Plasma/Correlation/crp/regression_plots/PON3_GPA_MPA_regression.pdf"))

create_crp_table <- function(source = "Plasma", marker = "crp", type = "GPA") {

  readxl::read_excel(paste0("~/Results/", source, "/Correlation/", marker, "/", marker, "_", type, "_pearson_correlation.xlsx")) %>%
  dplyr::select(-c(method, alternative)) %>%
  mutate_if(is.numeric, round, 3) %>%
  mutate("plot" = if(type == "GPA" | type == "MPA") { paste0('<a href ="./../Results/', source, '/Correlation/', marker, '/regression_plots/', Assay, '_GPA_MPA_regression.pdf"  target="_blank">', Assay, '</a>') } else { paste0('<a href ="./../Results/', source, '/Correlation/', marker, '/regression_plots/', Assay, '_MP_PR3_regression.png"  target="_blank">', Assay, '</a>')}) %>%
  datatable(class = 'cell-border stripe compact', 
            extensions = 'Buttons', 
            options = list(
              scrollX = TRUE,
              dom = 'Bfrtip',
              buttons = c('copy', 'csv', 'excel', 'pdf')),
            escape = FALSE)

}

::::: {.panelset}

::: {.panel} [GPA]{.panel-name}

create_crp_table("Plasma", "crp", "GPA")

:::

::: {.panel} [MPA]{.panel-name}

create_crp_table("Plasma", "crp", "MPA")

:::

::: {.panel} [MPO]{.panel-name}

create_crp_table("Plasma", "crp", "MPO")

:::

::: {.panel} [PR3]{.panel-name}

create_crp_table("Plasma", "crp", "PR3")

:::

:::::

sr

The full list of protein-wise Pearson correlation results for the different phenotypes with sr is collected in excel files in Results/Plasma/Correlation/sr/sr_phenotype_pearson_correlation.xlsx and shown in the table below.

All individuals regressions are plotted and collected in the subfolder regression_plots/ (see Figure \@ref(fig:srCorr)). MPA and GPA or MPO and PR3 are each plotted on the same plot, but visualized in a different color.

knitr::include_graphics(c("Results/Plasma/Correlation/sr/regression_plots/CCL18_PARC_GPA_MPA_regression.pdf", "Results/Plasma/Correlation/sr/regression_plots/CD6_GPA_MPA_regression.pdf"))

::::: {.panelset}

::: {.panel} [GPA]{.panel-name}

create_crp_table("Plasma", "sr", "GPA")

:::

::: {.panel} [MPA]{.panel-name}

create_crp_table("Plasma", "sr", "MPA")

:::

::: {.panel} [MPO]{.panel-name}

create_crp_table("Plasma", "sr", "MPO")

:::

::: {.panel} [PR3]{.panel-name}

create_crp_table("Plasma", "sr", "PR3")

:::

:::::

bvas

The full list of protein-wise Pearson correlation results for the different phenotypes with bvas is collected in excel files in Results/Plasma/Correlation/bvas/bvas_phenotype_pearson_correlation.xlsx and shown in the table below.

All individuals regressions are plotted and collected in the subfolder regression_plots/ (see example Figure \@ref(fig:bvasCorr)). MPA and GPA or MPO and PR3 are each plotted on the same plot, but visualized in a different color.

knitr::include_graphics(c("Results/Plasma/Correlation/bvas/regression_plots/ST2_GPA_MPA_regression.pdf", "Results/Plasma/Correlation/bvas/regression_plots/Flt3L_GPA_MPA_regression.pdf"))

::::: {.panelset}

::: {.panel} [GPA]{.panel-name}

create_crp_table("Plasma", "bvas", "GPA")

:::

::: {.panel} [MPA]{.panel-name}

create_crp_table("Plasma", "bvas", "MPA")

:::

::: {.panel} [MPO]{.panel-name}

create_crp_table("Plasma", "bvas", "MPO")

:::

::: {.panel} [PR3]{.panel-name}

create_crp_table("Plasma", "bvas", "PR3")

:::

:::::

Serum

crp

The full list of protein-wise Pearson correlation results for the different phenotypes with crp is collected in excel files in Results/Serum/Correlation/crp/crp_phenotype_pearson_correlation.xlsx and shown in the table below.

All individuals regressions are plotted and collected in the subfolder regression_plots/.

::::: {.panelset}

::: {.panel} [GPA]{.panel-name}

create_crp_table("Serum", "crp", "GPA")

:::

::: {.panel} [MPA]{.panel-name}

create_crp_table("Serum", "crp", "MPA")

:::

::: {.panel} [MPO]{.panel-name}

create_crp_table("Serum", "crp", "MPO")

:::

::: {.panel} [PR3]{.panel-name}

create_crp_table("Serum", "crp", "PR3")

:::

:::::

sr

The full list of protein-wise Pearson correlation results for the different phenotypes with sr is collected in excel files in Results/Serum/Correlation/sr/sr_phenotype_pearson_correlation.xlsx and shown in the table below.

All individuals regressions are plotted and collected in the subfolder regression_plots/.

::::: {.panelset}

::: {.panel} [GPA]{.panel-name}

create_crp_table("Serum", "sr", "GPA")

:::

::: {.panel} [MPA]{.panel-name}

create_crp_table("Serum", "sr", "MPA")

:::

::: {.panel} [MPO]{.panel-name}

create_crp_table("Serum", "sr", "MPO")

:::

::: {.panel} [PR3]{.panel-name}

create_crp_table("Serum", "sr", "PR3")

:::

:::::

bvas

The full list of protein-wise Pearson correlation results for the different phenotypes with bvas is collected in excel files in Results/Serum/Correlation/bvas/bvas_phenotype_pearson_correlation.xlsx and shown in the table below.

All individuals regressions are plotted and collected in the subfolder regression_plots/.

::::: {.panelset}

::: {.panel} [GPA]{.panel-name}

create_crp_table("Serum", "bvas", "GPA")

:::

::: {.panel} [MPA]{.panel-name}

create_crp_table("Serum", "bvas", "MPA")

:::

::: {.panel} [MPO]{.panel-name}

create_crp_table("Serum", "bvas", "MPO")

:::

::: {.panel} [PR3]{.panel-name}

create_crp_table("Serum", "bvas", "PR3")

:::

:::::

vincent-van-hoef/Analysis5204 documentation built on June 24, 2022, 2:41 p.m.